Releases | Open Source Science

Nextclade - 3.16.0

3.16.0

Introduce JSON Schema definitions

We now provide JSON Schema definitions for some of the JSON-based Nextclade file formats. You can find the latest definitions and documentation here. You can also generate schemas for your current version of Nextclade CLI using the newly added nextclade schema write command.

These schemas enable validation and parser code generation (among other things) to help in development and maintenance of projects using JSON-based Nextclade formats. We would like to emphasize that currently all JSON-based Nextclade formats are unstable and can change even in minor and patch releases. Addition of schemas don't change these stability guarantees, but could help in reducing and fixing breakage after breaking changes.

Implement amino acid mutation labels

We added functionality to detect labeled amino acid mutations if dataset authors choose to define labels for them. This is similar to the existing labeled nucleotide mutations functionality, but for amino acid sequences. This could be useful to mark particular mutations of interest. Once datasets start adopting this functionality (by adding configuration to the mutLabels.aaMutLabelMap in pathogen.json of a dataset), you can find the results in the privateAaMutations.labeledSubstitutions column/field of Nextclade output files.

### Installation and usage 📚 Documentation: [docs.nextstrain.org/projects/nextclade](https://docs.nextstrain.org/projects/nextclade) 🌍 Nextclade Web: [clades.nextstrain.org](https://clades.nextstrain.org) 🖥️ Nextclade CLI: - 📥 Standalone native executables can be downloaded using the links in the "Assets" section just below. Mind the different operating systems and computer architectures. - 🐋 Docker images are available on [DockerHub](https://hub.docker.com/r/nextstrain/nextclade) - 🐍 Conda package is available in [bioconda channel](https://bioconda.github.io/recipes/nextclade/README.html). ⌨️ Source code is on GitHub: [github.com/nextstrain/nextclade](https://github.com/nextstrain/nextclade) 🚩 Report bugs, suggest features by submitting a [GitHub issue](https://github.com/nextstrain/nextclade/issues) 💾 Nextclade datasets are [here](https://github.com/nextstrain/nextclade_data)

Scientific Software - Peer-reviewed - Rust
Published by nextstrain-bot 7 months ago

Nextclade - 3.15.3

3.15.3

fix: ensure GFF3 fields are correctly percent-encoded and decoded

GFF3 specification requires certain characters in values and in attributes to be encoded using percent-encoding. Nextclade previously did not comply with this requirement, which could lead to incorrectly formatted annotation-related outputs (such as annotation field in JSON output or values in GFF3 output annotation). This has been fixed.

### Installation and usage 📚 Documentation: [docs.nextstrain.org/projects/nextclade](https://docs.nextstrain.org/projects/nextclade) 🌍 Nextclade Web: [clades.nextstrain.org](https://clades.nextstrain.org) 🖥️ Nextclade CLI: - 📥 Standalone native executables can be downloaded using the links in the "Assets" section just below. Mind the different operating systems and computer architectures. - 🐋 Docker images are available on [DockerHub](https://hub.docker.com/r/nextstrain/nextclade) - 🐍 Conda package is available in [bioconda channel](https://bioconda.github.io/recipes/nextclade/README.html). ⌨️ Source code is on GitHub: [github.com/nextstrain/nextclade](https://github.com/nextstrain/nextclade) 🚩 Report bugs, suggest features by submitting a [GitHub issue](https://github.com/nextstrain/nextclade/issues) 💾 Nextclade datasets are [here](https://github.com/nextstrain/nextclade_data)

Scientific Software - Peer-reviewed - Rust
Published by nextstrain-bot 8 months ago

Nextclade - 3.15.2

3.15.2

fix: calculate phenotypes even if there's no tree

Nextclade now calculates and displays phenotype data even for datasets which have no reference tree. The clade ignoring feature does not apply for such datasets (because no clade assignment is possible without a tree).

fix: collapse -0.0 to 0.0 in phenotype values

Nextclade will no longer display or output negative zeroes in phenotype data.

fix: ensure CSV column and category selection is additive

Nextclade now correctly adds all entries together, when mixing individual columns and column categories in CSV and TSV output columns selection configuration (e.g. in --output-columns-selection CLI argument). Previously one would incorrectly overwrite the other.

fix: ensure canonical order of CSV columns

Order of columns in CSV and TSV is now always enforced to be the same, regardless of presence or absence of certain columns.

### Installation and usage 📚 Documentation: [docs.nextstrain.org/projects/nextclade](https://docs.nextstrain.org/projects/nextclade) 🌍 Nextclade Web: [clades.nextstrain.org](https://clades.nextstrain.org) 🖥️ Nextclade CLI: - 📥 Standalone native executables can be downloaded using the links in the "Assets" section just below. Mind the different operating systems and computer architectures. - 🐋 Docker images are available on [DockerHub](https://hub.docker.com/r/nextstrain/nextclade) - 🐍 Conda package is available in [bioconda channel](https://bioconda.github.io/recipes/nextclade/README.html). ⌨️ Source code is on GitHub: [github.com/nextstrain/nextclade](https://github.com/nextstrain/nextclade) 🚩 Report bugs, suggest features by submitting a [GitHub issue](https://github.com/nextstrain/nextclade/issues) 💾 Nextclade datasets are [here](https://github.com/nextstrain/nextclade_data)

Scientific Software - Peer-reviewed - Rust
Published by nextstrain-bot 8 months ago

Nextclade - 3.15.1

3.15.1

Nextclade Web: fix empty results table

Results table could sometimes be empty when starting Nextclade analysis from URL parameters. This have been fixed.

### Installation and usage 📚 Documentation: [docs.nextstrain.org/projects/nextclade](https://docs.nextstrain.org/projects/nextclade) 🌍 Nextclade Web: [clades.nextstrain.org](https://clades.nextstrain.org) 🖥️ Nextclade CLI: - 📥 Standalone native executables can be downloaded using the links in the "Assets" section just below. Mind the different operating systems and computer architectures. - 🐋 Docker images are available on [DockerHub](https://hub.docker.com/r/nextstrain/nextclade) - 🐍 Conda package is available in [bioconda channel](https://bioconda.github.io/recipes/nextclade/README.html). ⌨️ Source code is on GitHub: [github.com/nextstrain/nextclade](https://github.com/nextstrain/nextclade) 🚩 Report bugs, suggest features by submitting a [GitHub issue](https://github.com/nextstrain/nextclade/issues) 💾 Nextclade datasets are [here](https://github.com/nextstrain/nextclade_data)

Scientific Software - Peer-reviewed - Rust
Published by nextstrain-bot 9 months ago

Nextclade - 3.15.0

3.15.0 Nextclade Web: fix country colorings in output tree json #1646

Colors for "country", "region" and "division" are now correctly displayed in tree view

CDS coverage #1514

Nextclade now calculates amino acid coverage of each CDS. You can find this information:

in output files: in the column or field cdsCoverage
in Nextclade Web: in the tooltip of the "Cov." column on "Results" page

### Installation and usage 📚 Documentation: [docs.nextstrain.org/projects/nextclade](https://docs.nextstrain.org/projects/nextclade) 🌍 Nextclade Web: [clades.nextstrain.org](https://clades.nextstrain.org) 🖥️ Nextclade CLI: - 📥 Standalone native executables can be downloaded using the links in the "Assets" section just below. Mind the different operating systems and computer architectures. - 🐋 Docker images are available on [DockerHub](https://hub.docker.com/r/nextstrain/nextclade) - 🐍 Conda package is available in [bioconda channel](https://bioconda.github.io/recipes/nextclade/README.html). ⌨️ Source code is on GitHub: [github.com/nextstrain/nextclade](https://github.com/nextstrain/nextclade) 🚩 Report bugs, suggest features by submitting a [GitHub issue](https://github.com/nextstrain/nextclade/issues) 💾 Nextclade datasets are [here](https://github.com/nextstrain/nextclade_data)

Scientific Software - Peer-reviewed - Rust
Published by nextstrain-bot 9 months ago

Nextclade - 3.14.5

3.14.5

Nextclade Web: disable "Relative to" dropdown when dataset has no reference tree

When using a dataset without reference tree for analysis, the "Relative to" dropdown has no meaning - the target for comparisons is always reference sequence node, because there is no information about any other nodes. We now disable this dropdown for datasets without trees.

### Installation and usage 📚 Documentation: [docs.nextstrain.org/projects/nextclade](https://docs.nextstrain.org/projects/nextclade) 🌍 Nextclade Web: [clades.nextstrain.org](https://clades.nextstrain.org) 🖥️ Nextclade CLI: - 📥 Standalone native executables can be downloaded using the links in the "Assets" section just below. Mind the different operating systems and computer architectures. - 🐋 Docker images are available on [DockerHub](https://hub.docker.com/r/nextstrain/nextclade) - 🐍 Conda package is available in [bioconda channel](https://bioconda.github.io/recipes/nextclade/README.html). ⌨️ Source code is on GitHub: [github.com/nextstrain/nextclade](https://github.com/nextstrain/nextclade) 🚩 Report bugs, suggest features by submitting a [GitHub issue](https://github.com/nextstrain/nextclade/issues) 💾 Nextclade datasets are [here](https://github.com/nextstrain/nextclade_data)

Scientific Software - Peer-reviewed - Rust
Published by nextstrain-bot 9 months ago

Nextclade - 3.14.4

3.14.4

Fix seed coverage calculation for short references

During alignment, seed coverage is now computed as the total seed length divided by the shorter of the query or reference. This ensures correct behavior when references are shorter than queries, without requiring artificially low min_seed_cover values.

Nextclade Web: fix crash when using `?multi-dataset` URL parameter

When used ?multi-dataset URL parameter, Nextclade Web could crash under certain conditions. This has been fixed.

Nextclade Web: workaround double run

When using URL parameters, Nextclade could sometimes spawn multiple copies of the analysis run. This could result in duplicated sequences being reported in the results table erroneously as well as in other unwanted effects. We added a workaround to mitigate this problem. Please report bugs by submitting a GitHub issue.

### Installation and usage 📚 Documentation: [docs.nextstrain.org/projects/nextclade](https://docs.nextstrain.org/projects/nextclade) 🌍 Nextclade Web: [clades.nextstrain.org](https://clades.nextstrain.org) 🖥️ Nextclade CLI: - 📥 Standalone native executables can be downloaded using the links in the "Assets" section just below. Mind the different operating systems and computer architectures. - 🐋 Docker images are available on [DockerHub](https://hub.docker.com/r/nextstrain/nextclade) - 🐍 Conda package is available in [bioconda channel](https://bioconda.github.io/recipes/nextclade/README.html). ⌨️ Source code is on GitHub: [github.com/nextstrain/nextclade](https://github.com/nextstrain/nextclade) 🚩 Report bugs, suggest features by submitting a [GitHub issue](https://github.com/nextstrain/nextclade/issues) 💾 Nextclade datasets are [here](https://github.com/nextstrain/nextclade_data)

Scientific Software - Peer-reviewed - Rust
Published by nextstrain-bot 9 months ago

Nextclade - 3.14.3

3.14.3

Fix dataset suggestions and sorting for short references

Update minimizer-based scoring to better handle cases where the reference sequence is much shorter than the query sequence. The previous approach assumed full-genome references and could underestimate scores for partial references such as single genes. The revised method adjusts the normalization to avoid penalizing such cases, improving robustness without requiring changes to the index format. This resolves issues observed in datasets like yellow fever.

This improves dataset suggestions in Nextclade Web and dataset detection in nextclade sort CLI command. This also changes the scale of values of column score in the TSV output of nextclade sort command.

### Installation and usage 📚 Documentation: [docs.nextstrain.org/projects/nextclade](https://docs.nextstrain.org/projects/nextclade) 🌍 Nextclade Web: [clades.nextstrain.org](https://clades.nextstrain.org) 🖥️ Nextclade CLI: - 📥 Standalone native executables can be downloaded using the links in the "Assets" section just below. Mind the different operating systems and computer architectures. - 🐋 Docker images are available on [DockerHub](https://hub.docker.com/r/nextstrain/nextclade) - 🐍 Conda package is available in [bioconda channel](https://bioconda.github.io/recipes/nextclade/README.html). ⌨️ Source code is on GitHub: [github.com/nextstrain/nextclade](https://github.com/nextstrain/nextclade) 🚩 Report bugs, suggest features by submitting a [GitHub issue](https://github.com/nextstrain/nextclade/issues) 💾 Nextclade datasets are [here](https://github.com/nextstrain/nextclade_data)

Scientific Software - Peer-reviewed - Rust
Published by nextstrain-bot 9 months ago

Nextclade - 3.14.2

3.14.2

Nextclade Web: crash with custom Auspice JSON dataset

When an Auspice JSON dataset is provided as whole-dataset input through ?dataset-json-url, Nextclade Web could crash under certain conditions. This has been fixed.

### Installation and usage 📚 Documentation: [docs.nextstrain.org/projects/nextclade](https://docs.nextstrain.org/projects/nextclade) 🌍 Nextclade Web: [clades.nextstrain.org](https://clades.nextstrain.org) 🖥️ Nextclade CLI: - 📥 Standalone native executables can be downloaded using the links in the "Assets" section just below. Mind the different operating systems and computer architectures. - 🐋 Docker images are available on [DockerHub](https://hub.docker.com/r/nextstrain/nextclade) - 🐍 Conda package is available in [bioconda channel](https://bioconda.github.io/recipes/nextclade/README.html). ⌨️ Source code is on GitHub: [github.com/nextstrain/nextclade](https://github.com/nextstrain/nextclade) 🚩 Report bugs, suggest features by submitting a [GitHub issue](https://github.com/nextstrain/nextclade/issues) 💾 Nextclade datasets are [here](https://github.com/nextstrain/nextclade_data)

Scientific Software - Peer-reviewed - Rust
Published by nextstrain-bot 9 months ago

Nextclade - 3.14.1

3.14.1

Nextclade Web: crash with custom datasets

When a custom dataset is provided through ?dataset-url, Nextclade Web could crash under certain conditions. This has been fixed. Issue PR

### Installation and usage 📚 Documentation: [docs.nextstrain.org/projects/nextclade](https://docs.nextstrain.org/projects/nextclade) 🌍 Nextclade Web: [clades.nextstrain.org](https://clades.nextstrain.org) 🖥️ Nextclade CLI: - 📥 Standalone native executables can be downloaded using the links in the "Assets" section just below. Mind the different operating systems and computer architectures. - 🐋 Docker images are available on [DockerHub](https://hub.docker.com/r/nextstrain/nextclade) - 🐍 Conda package is available in [bioconda channel](https://bioconda.github.io/recipes/nextclade/README.html). ⌨️ Source code is on GitHub: [github.com/nextstrain/nextclade](https://github.com/nextstrain/nextclade) 🚩 Report bugs, suggest features by submitting a [GitHub issue](https://github.com/nextstrain/nextclade/issues) 💾 Nextclade datasets are [here](https://github.com/nextstrain/nextclade_data)

Scientific Software - Peer-reviewed - Rust
Published by nextstrain-bot 9 months ago

Nextclade - 3.14.0

3.14.0

Nextclade Web: multi-dataset mode

Nextclade Web now allows to run analysis for multiple datasets at once.

You could provide sequences belonging to multiple organisms or for the same organism, but based on different reference sequences. On "Multiple datasets" tab, Nextclade will try to deduce datasets that are best matching your sequences. You can then proceed to running analysis for each dataset. If multiple datasets have been detected, you will see a "Dataset" dropdown on "Results", "Tree" and "Export" page, which allows you to switch between results for different datasets.

In multi-dataset mode, the "Export" page now also contains an "Export all to Excel" button, which allows to download .xlsx file containing all analysis results in tabular format, one dataset per sheet. This is the same data as in CSV/TSV files, but aggregated into a single file.

When starting Nextclade analysis using URL parameters, you can add ?multi-dataset to run in multi-dataset mode.

Nextclade is now using new global search algorithm to find the suggested datasets for your sequences. It tries to minimize the number of datasets, while optimizing their relevance.

This is a convenience feature, i.e. the analysis runs for each dataset are still independent, just like in single-dataset mode, except you don't need to run multiple analyses for each dataset manually now.

This could be useful if you analyze one or multiple a FASTA files containing a mixture of sequences obtained from different organisms, strains or genome segments.

Nextclade Web: add "Download SVG" button to "Tree" page

There is now a "Download SVG" button in the top-right corner of the "Tree" page. It allows to download the tree visualization and other contents of the page, including applied filters and zoom, to an SVG file. This functionality is similar to that is offered by Auspice.

Nextclade Web: add "Focus on selected" toggle on "Tree" page

Adds a sidebar toggle on "Tree" page that emphasizes visible nodes by expanding them to occupy more vertical space, improving focus on filtered or zoomed subsets. Designed to enhance visibility in large phylogenetic trees. This is an Auspice feature which was introduced in Auspice 2.59.0 and now also available in Nextclade.

Nextclade CLI: global dataset search mode for `sort` command

You can now add --global to sort command to enable global search algorithm to find the minimal set of suggested datasets for your sequences. Note that this mode disables streaming of results, because the optimization step requires knowing datasets for all sequences in advance. This may lead to increased memory consumption for large inputs.

This is an experimental feature. Use with caution.

Nextclade CLI: fix panics

Some of the expected errors (e.g. invalid input files) in Nextclade CLI would previously cause panics (crashes). Now these errors are handled more gracefully and the visual output of these errors to the console is now cleaner and more concise.

Nextclade CLI: fix console color mode handling

Nextclade CLI previously output colored messages (with ANSI sequences) even if output is not a TTY (e.g. redirected to a file). This has now been fixed.

For additional configuration, the CLI arguments have been added, as well as proper handling of environment variables typically used to control console coloring.

The following priority rules apply:

Nextclade detects output target (TTY or not) and outputs appropriately for the target by default
If any of the environment variables: COLOR (auto|always|never), NO_COLOR (set), CLICOLOR_FORCE=1 are found, then they override the default
If arguments --color=auto|always|never or --no-color (shortcut for --color=never) are found, they override the defaults and environment variables. If multiple --color or --no-color arguments present, then only the argument that comes last is taken into account.

Known issue: --help coloring is not affected by --color and --no-color arguments: #1629

### Installation and usage 📚 Documentation: [docs.nextstrain.org/projects/nextclade](https://docs.nextstrain.org/projects/nextclade) 🌍 Nextclade Web: [clades.nextstrain.org](https://clades.nextstrain.org) 🖥️ Nextclade CLI: - 📥 Standalone native executables can be downloaded using the links in the "Assets" section just below. Mind the different operating systems and computer architectures. - 🐋 Docker images are available on [DockerHub](https://hub.docker.com/r/nextstrain/nextclade) - 🐍 Conda package is available in [bioconda channel](https://bioconda.github.io/recipes/nextclade/README.html). ⌨️ Source code is on GitHub: [github.com/nextstrain/nextclade](https://github.com/nextstrain/nextclade) 🚩 Report bugs, suggest features by submitting a [GitHub issue](https://github.com/nextstrain/nextclade/issues) 💾 Nextclade datasets are [here](https://github.com/nextstrain/nextclade_data)

Scientific Software - Peer-reviewed - Rust
Published by nextstrain-bot 9 months ago

Nextclade - 3.13.3

3.13.3

Fix crash when exporting annotations for sequences with missing genes

Nextclade Web and CLI would crash when attempting to output GFF and TBL files where entire genes are unsequenced or otherwise missing. This has been fixed.

### Installation and usage 📚 Documentation: [docs.nextstrain.org/projects/nextclade](https://docs.nextstrain.org/projects/nextclade) 🌍 Nextclade Web: [clades.nextstrain.org](https://clades.nextstrain.org) 🖥️ Nextclade CLI: - 📥 Standalone native executables can be downloaded using the links in the "Assets" section just below. Mind the different operating systems and computer architectures. - 🐋 Docker images are available on [DockerHub](https://hub.docker.com/r/nextstrain/nextclade) - 🐍 Conda package is available in [bioconda channel](https://bioconda.github.io/recipes/nextclade/README.html). ⌨️ Source code is on GitHub: [github.com/nextstrain/nextclade](https://github.com/nextstrain/nextclade) 🚩 Report bugs, suggest features by submitting a [GitHub issue](https://github.com/nextstrain/nextclade/issues) 💾 Nextclade datasets are [here](https://github.com/nextstrain/nextclade_data)

Scientific Software - Peer-reviewed - Rust
Published by nextstrain-bot 10 months ago

Nextclade - 3.13.2

3.13.2

Speed up Nextclade web, fix crash when using files >45MB on Chromium v136 browsers

In recently releaed version 136, Chromium-based browsers (e.g. Chrome, Edge) reduced the maximum allowed fixed array size, causing Nextclade web to crash when files bigger than 46,505,915 bytes are used.

It turns out that avoiding the need for a large array gets rid of most of the delay between clicking "Run" and the start of the analysis. For files of ~60MB the time saved is on the order of 5 seconds. A small but noticeable performance win! See issue #1605 and PR #1606 for more details.

### Installation and usage 📚 Documentation: [docs.nextstrain.org/projects/nextclade](https://docs.nextstrain.org/projects/nextclade) 🌍 Nextclade Web: [clades.nextstrain.org](https://clades.nextstrain.org) 🖥️ Nextclade CLI: - 📥 Standalone native executables can be downloaded using the links in the "Assets" section just below. Mind the different operating systems and computer architectures. - 🐋 Docker images are available on [DockerHub](https://hub.docker.com/r/nextstrain/nextclade) - 🐍 Conda package is available in [bioconda channel](https://bioconda.github.io/recipes/nextclade/README.html). ⌨️ Source code is on GitHub: [github.com/nextstrain/nextclade](https://github.com/nextstrain/nextclade) 🚩 Report bugs, suggest features by submitting a [GitHub issue](https://github.com/nextstrain/nextclade/issues) 💾 Nextclade datasets are [here](https://github.com/nextstrain/nextclade_data)

Scientific Software - Peer-reviewed - Rust
Published by nextstrain-bot 10 months ago

Nextclade - 3.13.1

3.13.1

Fix crash on empty query annotations

For certain samples which end up with an empty output genome annotation Nextclade Web could crash. This is now resolved. See #1601,#1602. Thanks @theosanderson for reporting.

### Installation and usage 📚 Documentation: [docs.nextstrain.org/projects/nextclade](https://docs.nextstrain.org/projects/nextclade) 🌍 Nextclade Web: [clades.nextstrain.org](https://clades.nextstrain.org) 🖥️ Nextclade CLI: - 📥 Standalone native executables can be downloaded using the links in the "Assets" section just below. Mind the different operating systems and computer architectures. - 🐋 Docker images are available on [DockerHub](https://hub.docker.com/r/nextstrain/nextclade) - 🐍 Conda package is available in [bioconda channel](https://bioconda.github.io/recipes/nextclade/README.html). ⌨️ Source code is on GitHub: [github.com/nextstrain/nextclade](https://github.com/nextstrain/nextclade) 🚩 Report bugs, suggest features by submitting a [GitHub issue](https://github.com/nextstrain/nextclade/issues) 💾 Nextclade datasets are [here](https://github.com/nextstrain/nextclade_data)

Scientific Software - Peer-reviewed - Rust
Published by nextstrain-bot 10 months ago

Nextclade - 3.13.0

3.13.0

Output genome annotations

Nextclade now outputs genome annotations for each unaligned input sequence.

These annotations are derived from reference annotation (coming from a dataset or from --input-annotation), but with the ranges of genetic features (genes, CDSes) adjusted for unaligned input sequences. The word "unaligned" here refers to the input sequences being analyzed and before they are aligned, i.e. as they come in the input fasta file(s).

These annotations can serve as a starting point for submissions to genetic databases. They also allow to extract nucleotide sequences of genes and CDSes from unaligned sequences, if you need this. Note that the extraction from aligned sequences (as being output by Nextclade) can still be done using reference annotation.

Nextclade supports 2 formats for output annotations:

Genbank’s 5-column tab-delimited feature table (TBL) format (spec)
Generic Feature Format Version 3 (GFF3) (spec)

Both formats contain the same information, but GFF3 contains slightly more metadata due to this format being more flexible. Use one or the other, depending on your needs.

In Nextclade Web, these new output annotations can be downloaded on the "Export" page, in the nextclade.tbl and nextclade.gff sections.

In Nextclade CLI, if you are using --output-all the annotations are emitted into output directory as files nextclade.tbl and nextclade.gff. You can also add --output-annotation-tbl and/or --output-annotation-gff to override the path, or you can use only these parameters and omit --output-all, to emit only specified individual files (similar to all other --output-* parameters).

Please note that the annotations can only be output if there's a reference annotation on the input (from a dataset or from --input-annotation).

This feature is still in an experimental phase. Please report bugs by submitting a GitHub issue.

### Installation and usage 📚 Documentation: [docs.nextstrain.org/projects/nextclade](https://docs.nextstrain.org/projects/nextclade) 🌍 Nextclade Web: [clades.nextstrain.org](https://clades.nextstrain.org) 🖥️ Nextclade CLI: - 📥 Standalone native executables can be downloaded using the links in the "Assets" section just below. Mind the different operating systems and computer architectures. - 🐋 Docker images are available on [DockerHub](https://hub.docker.com/r/nextstrain/nextclade) - 🐍 Conda package is available in [bioconda channel](https://bioconda.github.io/recipes/nextclade/README.html). ⌨️ Source code is on GitHub: [github.com/nextstrain/nextclade](https://github.com/nextstrain/nextclade) 🚩 Report bugs, suggest features by submitting a [GitHub issue](https://github.com/nextstrain/nextclade/issues) 💾 Nextclade datasets are [here](https://github.com/nextstrain/nextclade_data)

Scientific Software - Peer-reviewed - Rust
Published by nextstrain-bot 11 months ago

Nextclade - 3.12.0

3.12.0

Forbid reference sequences with gaps

Starting from this version, Nextclade won't accept reference sequences (reference.fasta) which contain gap characters (-).

This is true for reference sequences in Nextclade datasets (provided as --input-dataset, --dataset-name in CLI, or ?input-dataset, ?dataset-name in web), Auspice JSON datasets (through --input-dataset-json or ?input-dataset-json) as well as for individually provided reference sequences, in absence of a dataset or when overriding its files (--input-ref, ?input-ref).

We could not find meaning for the gaps in reference sequences in the context of Nextclade (pairwise alignment and comparison of sequences to a reference). When a reference with gaps have been used, it could have been causing errors and even possibly produced incorrect results silently.

Starting from this version, Nextclade will now stop with an explicit error if it detects gaps in reference sequence. To resolve, please use a reference sequence without gaps, if possible, or notify dataset authors about the problem.

If you think that Nextclade needs to support reference sequences with gaps please submit a new issue and explain your use-case and motivation on GitHub: https://github.com/nextstrain/nextclade/issues

### Installation and usage 📚 Documentation: [docs.nextstrain.org/projects/nextclade](https://docs.nextstrain.org/projects/nextclade) 🌍 Nextclade Web: [clades.nextstrain.org](https://clades.nextstrain.org) 🖥️ Nextclade CLI: - 📥 Standalone native executables can be downloaded using the links in the "Assets" section just below. Mind the different operating systems and computer architectures. - 🐋 Docker images are available on [DockerHub](https://hub.docker.com/r/nextstrain/nextclade) - 🐍 Conda package is available in [bioconda channel](https://bioconda.github.io/recipes/nextclade/README.html).

Scientific Software - Peer-reviewed - Rust
Published by nextstrain-bot 11 months ago

Nextclade - 3.11.0

3.11.0

Alignment presets

Nextclade CLI now supports --alignment-preset argument, which switches between pre-defined sets of alignment parameters. Currently available values are: - default: Suitable for aligning very similar sequences (this is the default) - high-diversity: Suitable for more diverse viruses - short-sequences: Suitable for short and partial sequences

This is an experimental feature. Presets are subject to change.

Fix crash with empty reference sequence

Nextclade crashed when an empty reference sequence file is provided. Now Nextclade checks for this condition and reports a useful error message instead.

### Installation and usage 📚 Documentation: [docs.nextstrain.org/projects/nextclade](https://docs.nextstrain.org/projects/nextclade) 🌍 Nextclade Web: [clades.nextstrain.org](https://clades.nextstrain.org) 🖥️ Nextclade CLI: - 📥 Standalone native executables can be downloaded using the links in the "Assets" section just below. Mind the different operating systems and computer architectures. - 🐋 Docker images are available on [DockerHub](https://hub.docker.com/r/nextstrain/nextclade) - 🐍 Conda package is available in [bioconda channel](https://bioconda.github.io/recipes/nextclade/README.html).

Scientific Software - Peer-reviewed - Rust
Published by nextstrain-bot 12 months ago

Nextclade - 3.10.2

3.10.2

Correctly handle comments in GFF3 files

Nextclade sometimes reported an error in GFF3 files containing comments. This has been fixed now.

[cli] Fix verbosity CLI arguments

The Nextclade CLI arguments -v and -q were having no effect after a recent update. This has been fixed now.

### Installation and usage 📚 Documentation: [docs.nextstrain.org/projects/nextclade](https://docs.nextstrain.org/projects/nextclade) 🌍 Nextclade Web: [clades.nextstrain.org](https://clades.nextstrain.org) 🖥️ Nextclade CLI: - 📥 Standalone native executables can be downloaded using the links in the "Assets" section just below. Mind the different operating systems and computer architectures. - 🐋 Docker images are available on [DockerHub](https://hub.docker.com/r/nextstrain/nextclade) - 🐍 Conda package is available in [bioconda channel](https://bioconda.github.io/recipes/nextclade/README.html).

Scientific Software - Peer-reviewed - Rust
Published by nextstrain-bot about 1 year ago

Nextclade - 3.10.1

3.10.1

[web] Fetch custom inputs from URLs using correct "Accept" HTTP header

Fixes Nextclade Web adding header Accept: application/json, text/plain, */* when making GET HTTP requests when fetching input files from use-provided URLs. This caused problems when fetching files from sources which allow to choose between different file formats using Accept header. The response would come in JSON format and this is not what we want. Now we add Accept: text/plain, */*, preferentially fetching all inputs as plaintext, as intended.

### Installation and usage 📚 Documentation: [docs.nextstrain.org/projects/nextclade](https://docs.nextstrain.org/projects/nextclade) 🌍 Nextclade Web: [clades.nextstrain.org](https://clades.nextstrain.org) 🖥️ Nextclade CLI: - 📥 Standalone native executables can be downloaded using the links in the "Assets" section just below. Mind the different operating systems and computer architectures. - 🐋 Docker images are available on [DockerHub](https://hub.docker.com/r/nextstrain/nextclade) - 🐍 Conda package is available in [bioconda channel](https://bioconda.github.io/recipes/nextclade/README.html).

Scientific Software - Peer-reviewed - Rust
Published by nextstrain-bot about 1 year ago

Nextclade - 3.9.1

Nextclade 3.9.1

Fix: clade mismatch between placed node and parent node

This version addresses an issue when sometimes clade (or clade-like attribute, such as lineage) of the placed query node might not always match the clade of its parent.

The query node placement is adjusted during the greedy tree building, and sometimes the branch needs to be split and a new auxiliary internal node to be inserted to accommodate the new node. Previously, Nextclade would copy the clade of this internal node from the attachment target node. However, this is not always correct and can lead to mismatch between clade of the query node and of the new internal node.

In this version we added a voting mechanism, which calculates a mode of the clades involved: of the parent, target and query nodes. The same procedure is repeated for each clade-like attribute. After that, in some cases, branch labels also need to adjust their positions.

This should not change the clade assignment for query samples, but only the clades of the inserted auxiliary internal nodes, to make sure that the tree is consistent.

### Installation and usage 📚 Documentation: [docs.nextstrain.org/projects/nextclade](https://docs.nextstrain.org/projects/nextclade) 🌍 Nextclade Web: [clades.nextstrain.org](https://clades.nextstrain.org) 🖥️ Nextclade CLI: - 📥 Standalone native executables can be downloaded using the links in the "Assets" section just below. Mind the different operating systems and computer architectures. - 🐋 Docker images are available on [DockerHub](https://hub.docker.com/r/nextstrain/nextclade) - 🐍 Conda package is available in [bioconda channel](https://bioconda.github.io/recipes/nextclade/README.html).

Scientific Software - Peer-reviewed - Rust
Published by nextstrain-bot over 1 year ago

Nextclade - 3.9.0

Nextclade 3.9.0

Nextclade CLI: Obtain CA certificates from platform trust store; add `NEXTCLADE_EXTRA_CA_CERTS` / `--extra-ca-certs`

Nextclade CLI users have previously reported issues with CA certificates when fetching datasets from an organization's network (e.g. in a university or in a company).

Starting with this version, Nextclade CLI respects the OS-level trust store configurations. This includes private CAs and self-signed certificates. Ensures backward compatibility and functionality across different platforms, including those lacking a native trust store or with outdated ones.

We introduced a NEXTCLADE_EXTRA_CA_CERTS environment variable and --extra-ca-certs option which allow adding additional CA certificates to the trust store specifically for Nextclade, for when modifying the system's trust store isn't desirable/possible. See #1536 for more details.

Update Auspice tree visualization to 2.58.0

Auspice tree visualization package has been updated from 2.56.0 to 2.58.0. See Auspice changelog here.

### Installation and usage 📚 Documentation: [docs.nextstrain.org/projects/nextclade](https://docs.nextstrain.org/projects/nextclade) 🌍 Nextclade Web: [clades.nextstrain.org](https://clades.nextstrain.org) 🖥️ Nextclade CLI: - 📥 Standalone native executables can be downloaded using the links in the "Assets" section just below. Mind the different operating systems and computer architectures. - 🐋 Docker images are available on [DockerHub](https://hub.docker.com/r/nextstrain/nextclade) - 🐍 Conda package is available in [bioconda channel](https://bioconda.github.io/recipes/nextclade/README.html).

Scientific Software - Peer-reviewed - Rust
Published by nextstrain-bot over 1 year ago

Nextclade - 3.8.2

Nextclade 3.8.2

Fix detection of number of threads Nextclade Web

Sometimes Nextclade Web would detect incorrect number of available CPU threads and would create too many processing threads. This could cause additional overhead and slowdown the runs. We observed this behavior in non-chromium based browsers, such as Firefox and Safari. This has been fixed now. The number of threads has been clamped to 3 by default. You can modify this in "Settings" dialog.

### Installation and usage 📚 Documentation: [docs.nextstrain.org/projects/nextclade](https://docs.nextstrain.org/projects/nextclade) 🌍 Nextclade Web: [clades.nextstrain.org](https://clades.nextstrain.org) 🖥️ Nextclade CLI: - 📥 Standalone native executables can be downloaded using the links in the "Assets" section just below. Mind the different operating systems and computer architectures. - 🐋 Docker images are available on [DockerHub](https://hub.docker.com/r/nextstrain/nextclade) - 🐍 Conda package is available in [bioconda channel](https://bioconda.github.io/recipes/nextclade/README.html).

Scientific Software - Peer-reviewed - Rust
Published by nextstrain-bot over 1 year ago

Nextclade - 3.8.1

Nextclade 3.8.1

Fix crash when using column config

Since 3.8.0, Nextclade could crash when particular combinations of CSV/TSV columns selected in "Column config" tab on "Export" page in Nextclade Web or with --output-columns-selection argument in Nextclade CLI. This has been resolved.

Remove extra spaces in ref node selector

Remove extra spaces in the text of entries in the "Relative to" dropdown selector in Nextclade Web.

### Installation and usage 📚 Documentation: [docs.nextstrain.org/projects/nextclade](https://docs.nextstrain.org/projects/nextclade) 🌍 Nextclade Web: [clades.nextstrain.org](https://clades.nextstrain.org) 🖥️ Nextclade CLI: - 📥 Standalone native executables can be downloaded using the links in the "Assets" section just below. Mind the different operating systems and computer architectures. - 🐋 Docker images are available on [DockerHub](https://hub.docker.com/r/nextstrain/nextclade) - 🐍 Conda package is available in [bioconda channel](https://bioconda.github.io/recipes/nextclade/README.html).

Scientific Software - Peer-reviewed - Rust
Published by nextstrain-bot over 1 year ago

Nextclade - 3.8.0

Nextclade 3.8.0

Relative mutations

Nextclade now calls mutations relative to multiple targets. Additionally to previously available mutations relative to reference and mutations relative to parent tree node (private mutations), Nextclade now calls mutations relative to clade founder tree nodes, and relative to custom nodes of interest if defined in the dataset (e.g. vaccine strains).

Nextclade Web now has an additional dropdown selector for the target of mutation calling. Output files has new columns/fields for mutations relative to clade founders (founderMuts) as well as for mutations relative to custom nodes (relativeMutations).

See documentation for more details.

Update Auspice tree visualization to 2.56.0

Auspice tree visualization package has been updated from 2.55.0 to 2.56.0. See Auspice changelog here.

### Installation and usage 📚 Documentation: [docs.nextstrain.org/projects/nextclade](https://docs.nextstrain.org/projects/nextclade) 🌍 Nextclade Web: [clades.nextstrain.org](https://clades.nextstrain.org) 🖥️ Nextclade CLI: - 📥 Standalone native executables can be downloaded using the links in the "Assets" section just below. Mind the different operating systems and computer architectures. - 🐋 Docker images are available on [DockerHub](https://hub.docker.com/r/nextstrain/nextclade) - 🐍 Conda package is available in [bioconda channel](https://bioconda.github.io/recipes/nextclade/README.html).

Scientific Software - Peer-reviewed - Rust
Published by nextstrain-bot over 1 year ago

Nextclade - 3.7.4

Nextclade 3.7.4

Nextclade Web

Upgrade Auspice to 2.55.0, add polyfills

This definitively resolves crash due to missing JavaScript polyfills, which occurred in Nextclade Web 3.7.2

### Installation and usage 📚 Documentation: [docs.nextstrain.org/projects/nextclade](https://docs.nextstrain.org/projects/nextclade) 🌍 Nextclade Web: [clades.nextstrain.org](https://clades.nextstrain.org) 🖥️ Nextclade CLI: - 📥 Standalone native executables can be downloaded using the links in the "Assets" section just below. Mind the different operating systems and computer architectures. - 🐋 Docker images are available on [DockerHub](https://hub.docker.com/r/nextstrain/nextclade) - 🐍 Conda package is available in [bioconda channel](https://bioconda.github.io/recipes/nextclade/README.html).

Scientific Software - Peer-reviewed - Rust
Published by nextstrain-bot over 1 year ago

Nextclade - 3.7.3

Nextclade 3.7.3

Nextclade Web

Fix crash on tree page in Nextclade Web

Temporarily downgrade Auspice from 2.55.0 to 2.54.3 to prevent the tree page in Nextclade Web from crashing. The definitive fix will follow.

### Installation and usage 📚 Documentation: [docs.nextstrain.org/projects/nextclade](https://docs.nextstrain.org/projects/nextclade) 🌍 Nextclade Web: [clades.nextstrain.org](https://clades.nextstrain.org) 🖥️ Nextclade CLI: - 📥 Standalone native executables can be downloaded using the links in the "Assets" section just below. Mind the different operating systems and computer architectures. - 🐋 Docker images are available on [DockerHub](https://hub.docker.com/r/nextstrain/nextclade) - 🐍 Conda package is available in [bioconda channel](https://bioconda.github.io/recipes/nextclade/README.html).

Scientific Software - Peer-reviewed - Rust
Published by nextstrain-bot over 1 year ago

Nextclade - 3.7.2

Nextclade 3.7.2

General

[fix] Avoid duplicate node names in the output Auspice JSON tree

When multiple query samples were to be placed onto the same node on the reference tree, sometimes multiple auxiliary nodes could be created having the same name. Node names are expected to be unique for Auspice visualization to work correctly, so when visualizing the tree Auspice have been renaming these nodes and emitting warnings into browsers' dev console.

In this version we pick unique names for the auxiliary nodes during placement, so that there are no more warnings. Users may observe changes in some of the node names when inspecting output Auspice JSON file. However, this unlikely to affect most users' work.

Nextclade Web

[fix] Ensure dataset "updated at" date is displayed in Nextclade Web

Since 3.7.0 Nextclade Web is not showing "updated at" date for any datasets. This has been fixed.

[fix] Ensure frame shift and insertion markers in sequence views can also be toggled

Most markers can be toggled on or off on the sequence views in "Settings" page in Nextclade Web, however frame shifts and insertions could not be. We added the missing toggles.

[fix] Correctly style details/summary component

The text in details/summary ("collapse", "spoiler") component (e.g. the list of SC2 lineages) overflowing and producing garbled text in dataset readmes and changelogs. This has been fixed.

[dep] Update Auspice tree visualization to 2.55.0

Auspice tree visualization package has been updated from 2.53.0 to 2.55.0. See Auspice changelog here.

Internal

[infra] Fix feature-policy and permission-policy HTTP headers

The deprecated feature-policy header was removed entirely and interest-cohort entry was removed from the permission-policy header. Latest versions of web browsers should no longer emit warnings into console.

[test] Test Nextclade CLI on more Linx distros

Additionally to the previous, we now test Nextclade CLI on the following newer Linux distributions:

Amazon Linux 2.0.2024
Debian 12
Fedora 41
Oracle Linux 8.9
Ubuntu 24.04

### Installation and usage 📚 Documentation: [docs.nextstrain.org/projects/nextclade](https://docs.nextstrain.org/projects/nextclade) 🌍 Nextclade Web: [clades.nextstrain.org](https://clades.nextstrain.org) 🖥️ Nextclade CLI: - 📥 Standalone native executables can be downloaded using the links in the "Assets" section just below. Mind the different operating systems and computer architectures. - 🐋 Docker images are available on [DockerHub](https://hub.docker.com/r/nextstrain/nextclade) - 🐍 Conda package is available in [bioconda channel](https://bioconda.github.io/recipes/nextclade/README.html).

Scientific Software - Peer-reviewed - Rust
Published by nextstrain-bot over 1 year ago

Nextclade - 3.7.1

Nextclade 3.7.1

Warn if reference sequence does not match root sequence of the tree

When both a standalone reference sequence and Auspice tree containing .root.sequence.nuc are present, Nextclade will check that these are the same sequence. If not, a warning is emitted to stderr for Nextclade CLI and to browser's dev console for Nextclade Web. This is mostly useful for dataset authors, for debugging.

Fix error when selecting a CDS in genome annotation visualization in Nextclade Web

Nextclade sometimes displayed an error in the peptide view when switching CDS by clicking on annotation visualization. This has been fixed now.

### Installation and usage 📚 Documentation: [docs.nextstrain.org/projects/nextclade](https://docs.nextstrain.org/projects/nextclade) 🌍 Nextclade Web: [clades.nextstrain.org](https://clades.nextstrain.org) 🖥️ Nextclade CLI: - 📥 Standalone native executables can be downloaded using the links in the "Assets" section just below. Mind the different operating systems and computer architectures. - 🐋 Docker images are available on [DockerHub](https://hub.docker.com/r/nextstrain/nextclade) - 🐍 Conda package is available in [bioconda channel](https://bioconda.github.io/recipes/nextclade/README.html).

Scientific Software - Peer-reviewed - Rust
Published by nextstrain-bot over 1 year ago

Nextclade - 3.7.0

Nextclade 3.7.0

Use Auspice JSON as a full dataset (experimental)

Nextclade can now optionally use Auspice datasets (in Auspice v2 JSON format) not only as reference trees, but also as self-contained full Nextclade datasets. Nextclade will take pathogen info, genome annotation, reference sequence, and, of course, reference tree from Auspice JSON. No other files are needed. This allows to use almost any Auspice dataset (e.g. from nextstrain.org) as Nextclade dataset.

In Nextclade CLI, --input-dataset argument now also accepts a path to Auspice JSON file (in addition to accepting the usual paths to a dataset directory and zip archive)
Nextclade Web now has a new URL parameter dataset-json-url, which accepts a URL to Auspice JSON file or even to a dataset URL on nextstrain.org

This feature is currently in experimental stage. For details and discussion see PR #1455.

Make reference tree branch attributes optional

Nextclade now accepts Auspice JSONs without .branch_attrs on tree nodes.

Allow `index` and `seqName` in column selection

Previously, Nextclade treated output CSV/TSV columns index and seqName as mandatory and they were always present in the output files. In this release they are made configurable. One can:

in CLI: add or omit index and seqName values when using --output-columns-selection argument
in Web: tick or untick checkboxes for index and seqName in "Column config" tab of "Export" page

Add dataset capabilities

The table in the nextclade dataset list command now displays an additional column "capabilities", which lists dataset capabilities, i.e. whether dataset contains information allowing clade assignment, QC, etc. The same information is available in JSON format (unstable) if you pass --json flag.

### Installation and usage 📚 Documentation: [docs.nextstrain.org/projects/nextclade](https://docs.nextstrain.org/projects/nextclade) 🌍 Nextclade Web: [clades.nextstrain.org](https://clades.nextstrain.org) 🖥️ Nextclade CLI: - 📥 Standalone native executables can be downloaded using the links in the "Assets" section just below. Mind the different operating systems and computer architectures. - 🐋 Docker images are available on [DockerHub](https://hub.docker.com/r/nextstrain/nextclade) - 🐍 Conda package is available in [bioconda channel](https://bioconda.github.io/recipes/nextclade/README.html).

Scientific Software - Peer-reviewed - Rust
Published by nextstrain-bot over 1 year ago

Nextclade - 3.6.0

Nextclade 3.6.0

Make reference tree node attribute `clade_membership` optional

Previously Nextclade required clade information to be always present in the input reference tree in the form of the .node_attrs.clade_membership field on each tree node. However, for certain datasets we might not have or need clade information. Making such datasets required workarounds, such as adding an empty string to the clade_membership field.

In this version we make clade_membership field optional. This allows to make datasets without clades. This is useful when working with organisms for which clades don't make sense or for which the nomenclature is not sufficiently established. This is also useful for dataset authors, who can now bootstrap simple datasets without clades first and then add clades and other features gradually later.

With this change, if clade_membership is not present in the dataset's reference tree nodes, then

Clade assignment will not run
Any clade-related functionality will not work
Output JSON/NDJSON result entries will not contain clade field
Clade column in output CSV/TSV will be empty
Clade column in Nextclade Web will be empty

This change does not affect any other parts of the application. Notably, clade-like attributes (from .meta.extensions.nextclade.clade_node_attrs), if present, are still assigned and being written to the output as before.

### Installation and usage 📚 Documentation: [docs.nextstrain.org/projects/nextclade](https://docs.nextstrain.org/projects/nextclade) 🌍 Nextclade Web: [clades.nextstrain.org](https://clades.nextstrain.org) 🖥️ Nextclade CLI: - 📥 Standalone native executables can be downloaded using the links in the "Assets" section just below. Mind the different operating systems and computer architectures. - 🐋 Docker images are available on [DockerHub](https://hub.docker.com/r/nextstrain/nextclade) - 🐍 Conda package is available in [bioconda channel](https://bioconda.github.io/recipes/nextclade/README.html).

Scientific Software - Peer-reviewed - Rust
Published by nextstrain-bot almost 2 years ago

Nextclade - 3.5.0

Nextclade 3.5.0

Algorithm

Detect loss of amino acid motifs correctly

Nextclade sometimes failed to detect a motif loss if that motif was the only one in its category. This is now fixed and users could observe changes in detected lost motifs. This affects datasets using aaMotifs property in their pathogen.json file, notably the flu datasets.

Nextclade Web

Ensure currently selected dataset is reloaded when it changes remotely

When dataset-url URL parameter is provided Nextclade Web would not update the dataset's pathogen.json file when remote dataset changes without changing its version. This is now fixed. It only affected users providing custom datasets using dataset-url URL parameter.

General

Upgrade Auspice

The Auspice tree rendering package has been updated from version 2.52.1 to version 2.53.0. See the list of changes here

### Installation and usage 📚 Documentation: [docs.nextstrain.org/projects/nextclade](https://docs.nextstrain.org/projects/nextclade) 🌍 Nextclade Web: [clades.nextstrain.org](https://clades.nextstrain.org) 🖥️ Nextclade CLI: - 📥 Standalone native executables can be downloaded using the links in the "Assets" section just below. Mind the different operating systems and computer architectures. - 🐋 Docker images are available on [DockerHub](https://hub.docker.com/r/nextstrain/nextclade) - 🐍 Conda package is available in [bioconda channel](https://bioconda.github.io/recipes/nextclade/README.html).

Scientific Software - Peer-reviewed - Rust
Published by nextstrain-bot almost 2 years ago

Nextclade - 3.4.0

Nextclade 3.4.0

Nextclade Web

Remove redundant scrollbars in dataset names

In dataset selector, sometimes there were extra scrollbars displayed to the right of the dataset names. This has been fixed.

Select suggested dataset automatically when suggestion is triggered manually

When suggestion is triggered manually, using "Suggest" button on main page, Nextclade will now automatically select the best dataset as the current dataset. Previously this could only be done by clearing the current dataset first and then clicking "Suggest". When suggestion algorithm is triggered automatically, the behavior is unchanged - the dataset will not be selected.

Nextclade CLI

Don't read dataset's `tree.json` and `genome_annotation.gff3` unless they are declared

Nextclade CLI will no longer read tree.json and genome_annotation.gff3 from the dataset, unless they are declared in the pathogen.json. These are optional files and we cannot assume their presence or filenames.

Warn user if input dataset contains extra files

Nextclade CLI will warn users when input datasets contains extra files which are not declared in the dataset's pathogen.json, or if there's extra declarations of files in the pathogen.json, but the files are not actually present in the dataset. This is mostly only useful to dataset authors for debugging issues in their datasets.

Add Bioconda Linux ARM build

We added one more build variant to Bioconda distribution channel - for Linux operating system on 64-bit ARM hardware architecture. It uses nextclade-aarch64-unknown-linux-gnu executable underneath. This can be useful if you prefer to manage Nextclade CLI installation on your Linux ARM machine or in a Docker ARM container with Conda package manager. However, because Nextclade CLI is a self-contained single-file executable, we still recommend direct downloads from GitHub Releases rather than Conda or other installation methods.

### Installation and usage 📚 Documentation: [docs.nextstrain.org/projects/nextclade](https://docs.nextstrain.org/projects/nextclade) 🌍 Nextclade Web: [clades.nextstrain.org](https://clades.nextstrain.org) 🖥️ Nextclade CLI: - 📥 Standalone native executables can be downloaded using the links in the "Assets" section just below. Mind the different operating systems and computer architectures. - 🐋 Docker images are available on [DockerHub](https://hub.docker.com/r/nextstrain/nextclade) - 🐍 Conda package is available in [bioconda channel](https://bioconda.github.io/recipes/nextclade/README.html).

Scientific Software - Peer-reviewed - Rust
Published by nextstrain-bot almost 2 years ago

Nextclade - 3.3.1

Nextclade CLI 3.3.1

Fix crash when using `--verbosity` option

Nextclade was crashing with internal error when --verbosity option was present. This has been fixed.

### Installation and usage 📚 Documentation: [docs.nextstrain.org/projects/nextclade](https://docs.nextstrain.org/projects/nextclade) 🌍 Nextclade Web: [clades.nextstrain.org](https://clades.nextstrain.org) 🖥️ Nextclade CLI: - 📥 Standalone native executables can be downloaded using the links in the "Assets" section just below. Mind the different operating systems and computer architectures. - 🐋 Docker images are available on [DockerHub](https://hub.docker.com/r/nextstrain/nextclade) - 🐍 Conda package is available in [bioconda channel](https://bioconda.github.io/recipes/nextclade/README.html).

Scientific Software - Peer-reviewed - Rust
Published by nextstrain-bot almost 2 years ago

Nextclade - 3.3.0

Nextclade 3.3.0

General

Allow FASTA files with leading newlines

Previously Nextclade would report an error "Expected character '>' at record start" when input FASTA file contained trailing newline or when it was empty. This was fixed.

Nextclade Web

Don't run dataset suggestion when navigating to "Datasets" page

Dataset suggestion will no longer run each time "Datasets" page is opened

Upgrade Auspice tree renderer from version 2.51.0 to 2.52.1

See changelog here

### Installation and usage 📚 Documentation: [docs.nextstrain.org/projects/nextclade](https://docs.nextstrain.org/projects/nextclade) 🌍 Nextclade Web: [clades.nextstrain.org](https://clades.nextstrain.org) 🖥️ Nextclade CLI: - 📥 Standalone native executables can be downloaded using the links in the "Assets" section just below. Mind the different operating systems and computer architectures. - 🐋 Docker images are available on [DockerHub](https://hub.docker.com/r/nextstrain/nextclade) - 🐍 Conda package is available in [bioconda channel](https://bioconda.github.io/recipes/nextclade/README.html).

Scientific Software - Peer-reviewed - Rust
Published by nextstrain-bot almost 2 years ago

Nextclade - 3.2.1

Nextclade 3.2.1

Nextclade CLI

Fix "Dataset not found" error when using `nextclade dataset get` with `--tag` argument.

This fixes a bug in the dataset filtering logic causing "Dataset not found" error when even correct name and tag were requested using nextclade dataset get with --tag argument.

### Installation and usage 📚 Documentation: [docs.nextstrain.org/projects/nextclade](https://docs.nextstrain.org/projects/nextclade) 🌍 Nextclade Web: [clades.nextstrain.org](https://clades.nextstrain.org) 🖥️ Nextclade CLI: - 📥 Standalone native executables can be downloaded using the links in the "Assets" section just below. Mind the different operating systems and computer architectures. - 🐋 Docker images are available on [DockerHub](https://hub.docker.com/r/nextstrain/nextclade) - 🐍 Conda package is available in [bioconda channel](https://bioconda.github.io/recipes/nextclade/README.html).

Scientific Software - Peer-reviewed - Rust
Published by nextstrain-bot about 2 years ago

Nextclade - 3.2.0

Nextclade 3.2.0

General

Minimizer search algorithm configuration has been improved

Minimizer search algorithm used in dataset auto-suggestion in Nextclade Web as well as in sort command of Nextclade CLI.

The default value for minimum match score (--min-score) has been reduced from 0.3 to 0.1. The default value for minimum number of hits (--min-hits) required for a detection has been reduced from 10 to 5. This should allow to better handle more diverse viruses.

If there is a sufficiently large gap between dataset scores, the algorithm will now only consider the group of datasets before the gap. The gap size can be configured using --max-score-gap argument in Nextclade CLI. The default value is 0.2.

Additionally, in Nextclade CLI sort command the algorithm now chooses only the best matching dataset. In order to select all matching datasets, the --all-matches flag has been added.

Nextclade CLI

Sequence index in the output TSV file of the `sort` command

The TSV output of the sort command (requested with --output-results-tsv) now contains additional column: index. The cells under this column contain index of the corresponding input sequence in the FASTA file. These indices can be used in the downstream processing to reliably map input sequences to the output results. Sequence names alone can be unreliable because they are arbitrary strings which are not guaranteed to be unique.

### Installation and usage 📚 Documentation: [docs.nextstrain.org/projects/nextclade](https://docs.nextstrain.org/projects/nextclade) 🌍 Nextclade Web: [clades.nextstrain.org](https://clades.nextstrain.org) 🖥️ Nextclade CLI: - 📥 Standalone native executables can be downloaded using the links in the "Assets" section just below. Mind the different operating systems and computer architectures. - 🐋 Docker images are available on [DockerHub](https://hub.docker.com/r/nextstrain/nextclade) - 🐍 Conda package is available in [bioconda channel](https://bioconda.github.io/recipes/nextclade/README.html).

Scientific Software - Peer-reviewed - Rust
Published by nextstrain-bot about 2 years ago

Nextclade - 3.1.0

CLI

PCR primers are back in Nextclade CLI

Due to popular demand, we are bringing back --input-pcr-primers argument for Nextclade CLI, which accepts a path to primers.csv file. The feature works just like it did prior to release of Nextclade v3, except primers.csv is never read from a dataset - you always need to provide it separately. At the same time, we removed support for primers field from pathogen.json, because it was too difficult to make a correct JSON object and it would conflict with the primers provided with --input-pcr-primers.

Web

Fix results table stripes

Results table stripes are always alternating now, regardless of sorting and filtering applied. This is only a visual change and does not affect any functionality.

### Installation and usage 📚 Documentation: [docs.nextstrain.org/projects/nextclade](https://docs.nextstrain.org/projects/nextclade) 🌍 Nextclade Web: [clades.nextstrain.org](https://clades.nextstrain.org) 🖥️ Nextclade CLI: - 📥 Standalone native executables can be downloaded using the links in the "Assets" section just below. Mind the different operating systems and computer architectures. - 🐋 Docker images are available on [DockerHub](https://hub.docker.com/r/nextstrain/nextclade) - 🐍 Conda package is available in [bioconda channel](https://bioconda.github.io/recipes/nextclade/README.html).

Scientific Software - Peer-reviewed - Rust
Published by nextstrain-bot about 2 years ago

Nextclade - 3.0.1

CLI

Bug fixes

Fixed a bug introduced in v3.0.0 which caused the default path for translations to be incorrect. This affected only users who used --output-all without passing a custom path template via --output-translations. The new default path is nextclade.cds_translation.{cds}.fasta where {cds} gets replaced with the name of the CDS, e.g. nextclade.cds_translation.S.fasta for SARS-CoV-2's spike protein.
Fixed a bug where nextclade dataset get command fails to download a dataset if a dataset has more than one version released.

Documentation

Added a section to the v3 migration guide about the renamed default path for translations, a breaking change. The new default output path for translations is nextclade.cds_translation.{cds}.fasta. Before v3, the default path was nextclade_gene_{gene}.translation.fasta. You can emulate the old (default) behavior by passing --output-translations="nextclade_gene_{cds}.translation.fasta" to nextclade3.

Instructions

📥 Nextclade CLI can be downloaded from the links in the "Assets" section just below. Note the difference in operating systems and computer architectures.

🌐 Nextclade Web is available at https://clades.nextstrain.org

🐋 Docker images are available at DockerHub

📚 To understand how it all works, make sure to read the Documentation

Scientific Software - Peer-reviewed - Rust
Published by nextstrain-bot about 2 years ago

Nextclade - 3.0.0

We are happy to present a major release of Nextclade, containing new features and bug fixes.

⚠️ This release contains breaking changes which may require your attention.

Useful links:

Nextclade Web v3
Nextclade Web v2 - if you need the old version, e.g. if you have custom v2 datasets
Nextclade CLI releases - all versions
Nextclade user documentation - for detailed instructions on how to use Nextclade Web and Nextclade CLI
Nextclade dataset curation guide - if you have a custom Nextclade dataset or want to create one
Nextclade source code repository - for contributors to Nextclade software (code, bug reports, feature requests etc.)
Nextclade data repository - for contributors to Nextclade datasets (add new datasets, update existing ones, report bugs, etc.)
Nextclade software issues - to report bugs and ask questions about Nextclade software
Nextclade data issues - to report bugs and ask questions about Nextclade datasets
Nextstrain discussion forum - for general discussion and questions about Nextstrain

BREAKING CHANGES

This section briefly lists breaking changes in Nextclade v3 compared to Nextclade v2. Please see Nextclade v3 migration guide (alternative link) for a detailed description of each breaking change and of possible migration paths.

Nextalign CLI is removed, because Nextclade CLI can now do everything that Nextalign v2 did
Potentially different alignment and translation output due to changes in the seed alignment algorithm. Some of the alignment parameters are removed. Default parameters of new parameters might need to be adjusted.
Potentially different tree output due to a new tree builder algorithm.
Dataset file format and dataset names have changed.
Some CLI arguments for individual input files are removed.
Some output files are removed
Genome annotation CLI argument is renamed
URL parameters in Nextclade Web have changed
CDS instead of genes

The sections below list all changes - breaking and non-breaking. The breaking changes are denoted with word [BREAKING].

If you encounter problems during migration, or breaking changes not mentioned in this document, please report it to the developers by opening a new GitHub issue.

General changes

[BREAKING] Alignment

The seed matching algorithm was rewritten to be more robust and handle sequences with higher diversity. For example, RSV-A can now be aligned against RSV-B.

Parameters minSeeds, seedLength, seedSpacing, minMatchRate, mismatchesAllowed, maxIndel no longer have any effect and are removed.

New parameters kmerLength, kmerDistance, minMatchLength, allowedMismatches, windowSize are added.

Default values should work for sequences with a diversity of up to X%. For sequences with higher diversity, the parameters may need to be adjusted.

For short sequences, the threshold length to use full-matrix alignment is now determined based on kmerLength instead of the removed seedLength. The coefficient is adjusted to roughly match the old final value.

Genome annotation

Replace genes with CDSes

Nextclade now treats genes only as containers for CDSes ("CDS" is coding sequence). CDSes are the main unit of translation and a basis for AA mutations now. A gene can contain multiple CDSes, but they are handled independently.

Handle fragmentation of genetic features

A CDS can consist of multiple fragments. These fragments are extracted from the full nucleotide genome independently and joined together (in the order provided in the genome annotation) to form the nucleotide sequence of the CDS. The CDS is then translated and the resulting polypeptides are analyzed (mutations are detected etc.). This implementation allows to handle slippage (e.g. ORF1ab in coronaviruses) and splicing (e.g. tat and rev in HIV-1).

Handle circular genomes

If genome annotation describes a CDS fragment as circular (wrapping around origin), Nextclade splits it into multiple linear (non-wrapping) fragments. The translation and analysis is then performed as if it was a linear genome.

Nextclade follows the GFF3 specification. Please refer to it for how to describe circular features.

Parse regions, genes and CDSes from GFF3 file

The GFF3 file parser has been augmented to support all the types of genetic features necessary for Nextclade to operate. There are still feature types which Nextclade ignores. We can consider supporting more types as scientific need arises.

Phylogenetic tree placement

Nextclade v3 now has the ability to phylogenetically resolve relationships between input sequences, where v2 would only attach each query sequence independently to the reference tree. Nextclade v3 thus may produce trees that are different from the trees produced in Nextclade v2.

Please read the Phylogenetic placement section in the documentation for more details.

Don't count mutations to ambiguous nucleotides as reversions

We no longer treat mutations to ambiguous nucleotides as reversions, i.e. if the attachment node has a mutation mutated with respect to reference and the query sequence is ambiguous we previously counted this as a reversion. This change only affects “private mutation” QC score and the classification of private mutations into “reversion substitution” and “unlabeled substitution”.

Changes in Nextclade Web

Dataset autosuggestion

Nextclade Web can now optionally suggest the most appropriate dataset(s) for user-provided input sequences. Drop your sequences and click "Suggest" to try out this feature.

Genome annotation widget

Following changes in genome annotation handling, the genome annotations widget in Nextclade Web now shows CDS fragments instead of genes.

CDS selector widget in Nextclade Web

The gene selector dropdown in Nextclade Web's results table has been transformed into a more general genetic feature selector. It shows the hierarchy of genetic features if there are nested features. Otherwise, the list is flat, to save screen space. It shows types of each of the genetic feature (gene, CDS or protein) as colorful badges. The menu is searchable, which is useful for mpox and other large viruses with many genes. Only CDSes can be selected currently, but we may extend this in the future to more feature types.

Show ambiguous nucleotides in sequence views

Nucleotide sequence views (in the results table) now also show colored markers for ambiguous nucleotides (non-ACTGN).

Improve website navigation

The row of buttons, containing "Back", "Tree" and other buttons is removed. Instead, different sections of the web application are always accessible via the main navigation bar.

The "Export" ("Download") and "Settings" sections are moved to dedicated pages.

[BREAKING] Changed and removed some of the URL parameters

Due to changes in the dataset format and input files, the URL parameters have the following changes:

input-root-seq renamed to input-ref
input-gene-map renamed to input-annotation
input-pathogen-json added
input-qc-config removed
input-pcr-primers removed
input-virus-properties removed
dataset-reference removed

[BREAKING] Removed some redundant output files

The nextclade.errors.csv and nextclade.insertions.csv files are removed and no longer appear in the "Export" dialog, nor are they included into the nextclade.zip archive of all outputs.

Errors and insertions are now included in the nextclade.csv and nextclade.tsv files.

Auspice updated from v2.45.2 to v2.51.0

The Auspice tree viewer component is updated from version 2.45.2 to 2.51.0. See the Auspice releases or changelog.

Changes in Nextclade CLI

[BREAKING] Nextalign CLI is removed

Nextalign CLI is no longer provided as a standalone application along with Nextclade CLI v3 because Nextclade now has all the features that distinguished Nextalign. This means there's only one set of command line arguments to remember. Nextclade CLI runs the same algorithms, accepts same the inputs and provides the same outputs as v2 Nextalign, plus some more. For most use-cases, the CLI interface and the input and output files should be the same or very similar.

[BREAKING] Some alignment parameters are removed

Due to changes in the seed alignment algorithm, the following parameters are no longer used and the corresponding CLI arguments and JSON fields under alignmentParams in pathogen.json (previously virus_properties.json) were removed:

text --seed-length --seed-spacing --max-indel --min-match-rate --min-seeds --mismatches-allowed

The following new alignment parameters were added:

text --allowed-mismatches --kmer-distance --kmer-length --min-match-length --min-seed-cover --max-alignment-attempts --max-band-area --window-size

[BREAKING] Some CLI arguments for individual input files are removed

Due to changes in the dataset format the following CLI arguments were removed:

text --input-virus-properties --input-qc-config --input-pcr-primers

in favor of --input-pathogen-json.

[BREAKING] Some CLI arguments for output files are removed

The arguments --output-errors and --output-insertions have been removed. Their information is now included in --output-csv and --output-tsv.

[BREAKING] Genome annotation CLI argument is renamed

The argument --input-gene-map renamed to --input-annotation. The short form -m remains unchanged.

[Breaking] Translation selection CLI argument is renamed

The argument --genes is renamed to --cds-selection. The short form -g remains unchanged.

Newick tree output

Nextclade can now also export the tree in Newick format via the --output-tree-nwk argument.

Optional input files

Most input files and files inside datasets are now optional. This simplifies dataset creation and maintenance and allows for step-by-step, incremental extension of them. You can start only with a reference sequence, which will only allow for alignment and very basic mutation calling in Nextclade, and later you can add more functionality. Optional input files also enable the removal of Nextalign CLI.

If you maintain a custom dataset or want to try creating one - refer to our Dataset curation guide. Community contributed datasets are welcome!

Added flag for disabling the new tree builder

The old phylogenetic tree placement behavior can be restored by adding the --without-greedy-tree-builder flag.

New arguments in `dataset list` command

The new argument --only-names allows to print a concise list of dataset names:

bash nextclade dataset list --only-names

The new argument --search allows to search datasets using substring match with dataset name, dataset friendly name, reference name or reference accession:

bash nextclade dataset list --search=flu

The argument --json allows to output a JSON object instead of the table. You can write it into a file and to postprocess it:

bash nextclade dataset list --json > "dataset_list.json" nextclade dataset list --json | jq '.[] | select(.path | startswith("nextstrain/sars-cov-2")) | .attributes'

New subcommand: `sort`

The sort subcommand takes your sequences in FASTA format and outputs sequences grouped by dataset in the form of a directory tree. Each subdirectory corresponds to a dataset and contains an output FASTA file with only sequences that are detected to be similar to the reference sequence in this dataset.

Example usage:

bash nextclade sort --output-dir="out/sort/" --output-results-tsv="out/sort.tsv" "input.fasta"

This can be useful for splitting FASTA files containing sequences which belong to different pathogens, strains or segments, for example for separating flu HA and NA segments.

New subcommand: `read-annotation`

The read-annotation subcommand takes a GFF3 file and displays how features are arranged hierarchically as viewed by Nextclade. This is useful for Nextclade developers and dataset creators to verify (and debug) how Nextclade understand genetic features from a particular GFF3 file.

Example usage:

bash nextclade read-annotation genome_annotation.gff3

Type nextclade read-annotation --help for description of arguments.

Performance improvements

Nextclade web now twice as fast when processing many sequences

Nextclade Web now uses multithreading more effectively. This results in faster processing of large fastas on computers with more than one processor. The speedup is around 2 for 1000 SARS-CoV-2 sequences on a multi-core machine.

Internal changes

Ensure type safety across programming language boundaries

The new features caused changes in major internal data structures and made them more complex. We now generate JSON schema and Typescript typings from Rust code. This allows to find mismatches between parts written in different languages, and to avoid bugs related to data types.

Make positions and ranges in different coord spaces type-safe

The change in genome annotation handling had significant consequences for coordinate spaces Nextclade is using internally (e.g. alignment space vs reference space, nuc space vs aa space, global nuc space vs nuc space local to a CDS). In order to make coordinate transforms safer, we introduced new Position and Range types, different for each space. This prevents mixing up coordinates in different spaces.

Instructions

📥 Nextclade CLI & Nextalign CLI can be downloaded from the links in the "Assets" section just below. Click "Show all" at the bottom of the "Assets" section to show more download options. Note the difference between "nextalign" and "nextclade" files as well as differences in operating systems and computer architectures.

🌐 Nextclade Web is available at https://clades.nextstrain.org

🐋 Docker images are available at DockerHub

📚 To understand how it all works, make sure to read the Documentation

Scientific Software - Peer-reviewed - Rust
Published by nextstrain-bot about 2 years ago

Nextclade - 3.0.0-alpha.2

| ⚠️ | This is a pre-release. It can contain bugs and significant changes which are not yet finalized. Changes may appear without notice. We recommend to try the pre-releases to learn about upcoming features. For important projects, use stable releases. | |:---:|:---|

For changes compared to the previous final release version, please refer to "Unreleased" section in CHANGELOG.md

Scientific Software - Peer-reviewed - Rust
Published by nextstrain-bot about 2 years ago

Nextclade - 3.0.0-alpha.1

| ⚠️ | This is a pre-release. It can contain bugs and significant changes which are not yet finalized. Changes may appear without notice. We recommend to try the pre-releases to learn about upcoming features. For important projects, use stable releases. | |:---:|:---|

For changes compared to the previous final release version, please refer to "Unreleased" section in CHANGELOG.md

Scientific Software - Peer-reviewed - Rust
Published by nextstrain-bot about 2 years ago

Nextclade - 3.0.0-alpha.0

| ⚠️ | This is a pre-release. It can contain bugs and significant changes which are not yet finalized. Changes may appear without notice. We recommend to try the pre-releases to learn about upcoming features. For important projects, use stable releases. | |:---:|:---|

For changes compared to the previous final release version, please refer to "Unreleased" section in CHANGELOG.md

Scientific Software - Peer-reviewed - Rust
Published by nextstrain-bot over 2 years ago

Nextclade - 2.14.0

Nextclade Web 2.14.0, Nextclade CLI 2.14.0 (2023-05-09)

Algorithm & Datasets: enable masked sites for distance calculation

For some viruses, genome sequencing is unreliable in specific parts of the genome or some regions should be ignored for other reasons when calculating distances between nodes for the purpose of placing query sequences on the reference tree. These distances are used to find the optimal (smallest distance) placement of the query sequence on the reference tree and sequence errors in these regions can lead to wrong placement.

Until now, to place query sequences on the reference tree, Nextclade counted all nucleotide differences between query and reference sequence. Moving forward, sequence regions to be ignored for reference tree placement can be defined in datasets' virus_properties.json. This is useful for example for SARS-CoV-2, where we will start ignoring the terminal parts of the untranslated regions. Another use case is mpox, where the terminal repeats are intrinsically constrained to be identical. Masking one of the two terminals will avoid double-counting of the same mutations.

PR #1128 adds this feature to Nextclade's algorithm.

Masked ranges are specified in the new field placementMaskRanges in datasets' virus_properties.json. For example, the terminal 50 nucleotides of SARS-CoV-2 can be ignored for tree placement by adding the following line (positions are 0-based and end-exclusive):

json "placementMaskRanges":[{"begin":0,"end":50},{"begin":29850,"end":29902}],

The changes are backwards compatible, if the field does not exist, Nextclade defaults to the old behavior of counting all nucleotide differences.

We are planning to shortly release a new version of SARS-CoV-2 datasets making use of this feature. Only a small proportion of sequences (<1%)should be affected, however where there are changes they will be a slight improvement in accuracy.

Avoid stale software and dataset versions in Nextclade Web

It was widely reported that users with long-persisting browser tabs and also users who don't switch datasets often, sometimes do not receive new Nextclade dataset updates, which meant that these users would not get newly designated lineages and clades lineage assignments.

Nextclade Web is a fully client-side, single-page application, which downloads the code and list of datasets once when first opening a tab. When users do not refresh the tab and don't change dataset, the same software and dataset version are used indefinitely. Without periodic page refresh and without periodic fetching of new dataset versions, users can run old code and use old data indefinitely, receiving obsolete or incomplete results.

In order to mitigate this problem, in this version, we add periodic background version checks in Nextclade Web. Every day or so, Nextclade Web will check whether the currently used version of software is the latest, as well as periodically refresh the list of available datasets and their versions. Whenever a new version of software or of a dataset is available, user will receive an update notification. The update can be accepted or dismissed (until the next version is available). Additionally, one can always obtain the latest code and datasets by doing a simple page reload in the browser (no need to clear the cache).

Nextclade is a fast-moving project, where new features and bug fixes are added frequently. We emphasize importance of using the latest versions of both, software and datasets, to receive the most accurate and up-to-date results.

Sort empty values in the results table in Nextclade Web

Nextclade Web previously had a bug, sorting incorrectly when the the column to be sorted by contained empty values. Empty values are now treated as empty strings, fixing this issue.

Improved citation dialog, website copy and translation in Nextclade Web

The "Citation" modal is now more readable and translated to multiple languages. We also added missing translations for some of the sentences in Nextclade Web. We made the intro text on main page of Nextclade Web more relevant.

Internal changes

Prevent duplicated GitHub action runs in pull requests
Remove Red Hat 7 from tested Linux distros
Fix Debian repositories in CI builds for aarch64-unknown-linux-gnu architecture
Update master branch of the fork before making bioconda PR branch
Extend dev documentation

Commit history

(click to expand)

Instructions

📥 Nextclade CLI & Nextalign CLI can be downloaded from the links in the "Assets" section just below. Click "Show all" at the bottom of the "Assets" section to show more download options. Note the difference between "nextalign" and "nextclade" files as well as differences in operating systems and computer architectures.

🌐 Nextclade Web is available at https://clades.nextstrain.org

🐋 Docker images are available at DockerHub

📚 To understand how it all works, make sure to read the Documentation

Scientific Software - Peer-reviewed - Rust
Published by nextstrain-bot almost 3 years ago

Nextclade - 2.13.1

Nextclade CLI 2.13.1 (2023-03-28)

Lower verbosity level of translation-related warnings in Nextclade CLI

Warnings related to translation of peptides now have verbosity level "info", down from "warning", to reduce clutter in logs. You can still find all errors and warnings in the "errors" and "warnings" columns of the CSV and TSV output files, as well as in the corresponding fields of JSON output files. If you want these warnings to be printed into the console, you can increase Nextclade CLI verbosity level to "info" by adding at least one occurrence of --verbose (-v) flag or by explicitly setting --verbosity=info or to a lower value. Type nextclade run --help for more details.

Internal changes

Add more smoke tests, including for datasets with default reference

Commit history

(click to expand)

Instructions

📥 Nextclade CLI & Nextalign CLI can be downloaded from the links in the "Assets" section just below. Click "Show all" at the bottom of the "Assets" section to show more download options. Note the difference between "nextalign" and "nextclade" files as well as differences in operating systems and computer architectures.

🌐 Nextclade Web is available at https://clades.nextstrain.org

🐋 Docker images are available at DockerHub

📚 To understand how it all works, make sure to read the Documentation

Scientific Software - Peer-reviewed - Rust
Published by nextstrain-bot almost 3 years ago

Nextclade - 2.13.0

Nextclade Web 2.13.0, Nextclade CLI 2.13.0 (2023-03-21)

Attach sequences to a priori most likely node if reference tree contains "placement_prior"

Until now, when there were multiple positions with equal numbers of mismatches between a query sequence and reference tree position, Nextclade always attached the query sequence to the reference tree node with the fewest number of ancestors. Due to the way recombinants are placed in the SARS-CoV-2 reference trees, this meant that in particular partial sequences were often attached to recombinants. With most recombinants being rare, this bias to attach to recombinants was often surprising.

In this version, we introduce a new feature that allows to attach sequences to a priori most likely nodes - taking into account which positions on the reference tree are most commonly found in circulation. The information on the prior probability that a particular reference tree node is the best match for a random query sequence is contained in the placement_prior reference tree node attribute. This attribute is currently only present in the most recent SARS-CoV-2 reference trees. The calculation can be found in this nextclade_data_workflows pull request.

To give an example: a partial sequence may have as many mismatches when compared to BA.5 as it has to the recombinant XP. Based on sequences in public databases, we know that BA.5 is much more common than XP. Hence, the query sequence is attached to BA.5. Previously, the query sequence would have been attached to XP, because XP has fewer parent nodes in the reference tree.

The impact of the feature is biggest for partial and incomplete sequences.

Add custom phenotype values to the newly placed tree nodes

When available in the dataset, the phenotype values (such as ace2_binding and immune_escape) are written into all output files except Auspice tree JSON. This omission is now fixed, and these values are set as tree node attributes. This allows to see the values and colorings for phenotype values on the tree page, and when loading the output tree JSON file into Auspice.

Fix length of 3' unsequenced aminoacid ranges in Nextclade Web

Nextclade Web was showing right boundary of the unsequenced AA range on the 3' end of peptide sequences incorrectly - the range was longer than expected. The calculations were using length of a gene in nucleotides, where there should be length in codons. This is now fixed.

Fix incorrect indices in mutation badges

The mutation badges in various places in Nextclade Web could show position "0", even though they are supposed to be 1-based. This was due to a programming mistake, which is now corrected.

Fix `input-pcr-primers` and `input-virus-properties` URL params in Nextclade Web

The input-pcr-primers and input-virus-properties URL params were swapped in the code accidentally, so one was incorrectly setting the other. This is now fixed.

Ensure translation warnings in CLI

Due to an omission, Nextclade CLI and Nextalign CLI since v2 did not print sequence translation-related warnings to the console. This is now fixed.

Fix Google Search Console warnings

We resolved warnings in Google Search Console: added canonical URL meta tag, and added noindex tag for non-release deployments. This should improve Nextclade appearance in Google Search.

Internal changes:

freeze wasm-pack version to 0.10.3

Commit history

(click to expand)

Instructions

📥 Nextclade CLI & Nextalign CLI can be downloaded from the links in the "Assets" section just below. Click "Show all" at the bottom of the "Assets" section to show more download options. Note the difference between "nextalign" and "nextclade" files as well as differences in operating systems and computer architectures.

🌐 Nextclade Web is available at https://clades.nextstrain.org

🐋 Docker images are available at DockerHub

📚 To understand how it all works, make sure to read the Documentation

Scientific Software - Peer-reviewed - Rust
Published by nextstrain-bot almost 3 years ago

Nextclade - 2.12.0

Nextclade Web 2.12.0, Nextclade CLI 2.12.0 (2023-02-28)

Improve tooltip for "missing" column in Nextclade Web

This column's tooltip now also shows ranges of unsequenced regions, i.e. contiguous ranges of nucleotide characters absent at the 5' and 3' end of the original query sequence, as compared to the reference sequence. To put it differently, these are the ranges that are to the left and right of the alignment range - from 0 to alignmentStart and from alignmentEnd to the length of the reference sequence. These regions may appear after alignment step, where Nextclade or Nextalign might insert characters - on the 5' and 3' ends to fill the query sequence to the length of the reference sequence. Just like it does with the characters that are absent from the inner parts of the query sequence (which we then call "deletions"). If found, the unsequenced regions are also shown as two light-grey rectangles at either or both ends of the sequence in sequence view column in Nextclade Web.

Unsequenced regions are not to be confused with the missing nucleotides, which are also shown in the same tooltip. Missing nucleotides are the N characters present in the original query sequence. They are not introduced nor modified by Nextclade and Nextalign, and are only detected and counted.

It seems that there is no consensus in the bioinformatics community about the notation and naming of either of these events (e.g. which character to use and how to call these ranges). Be thoughtful about these regions when working with the results of Nextclade and Nextalign, especially if you analyze:

sequences from different sources (different labs may use different conventions)
sequences that are partial (have large unsequenced ranges on 5' and 3' end and large deletions in the body)
sequences of low quality (e.g. lots of Ns and large deletions in the body)
sequences that are already aligned (e.g. have some form of padding on 5' and 3' ends)
sequences that are processed in some way (e.g. replacement or filling with N or -, or even filling from a consensus genome)

If you find strange or inconsistent results, we encourage you to inspect the input and output sequences in an alignment viewer on per-sequence basis and to contact the authors of individual sequences to clarify their conventions and intent.

Fix alignment range in CSV and TSV outputs

In CSV and TSV outputs, the values in columns alignmentStart and alignmentEnd were emitted in 0-based numbering. This was unexpected - by convention, CSV and TSV files have all ranges in 1-based format. This is now fixed.

Add new columns in CSV and TSV outputs

We added new columns in CSV and TSV outputs:

unknownAaRanges - list of detected contiguous ranges of unknown aminoacid (character X)
totalUnknownAa - total number of unknown aminoacids (character X)

Internal changes

Upgrade Auspice to 2.43.0 (changelog)
Upgrade Rust to 1.67.1 (changelog)

Commit history

(click to expand)

Instructions

📥 Nextclade CLI & Nextalign CLI can be downloaded from the links in the "Assets" section just below. Click "Show all" at the bottom of the "Assets" section to show more download options. Note the difference between "nextalign" and "nextclade" files as well as differences in operating systems and computer architectures.

🌐 Nextclade Web is available at https://clades.nextstrain.org

🐋 Docker images are available at DockerHub

📚 To understand how it all works, make sure to read the Documentation

Scientific Software - Peer-reviewed - Rust
Published by nextstrain-bot about 3 years ago

Nextclade - 2.11.0

Nextclade Web 2.11.0, Nextclade CLI 2.11.0 (2023-01-31)

IMPORTANT: ensure `index` column is written to CSV/TSV output files in case of error

The new column index was correctly written when analysis of a sample succeeds. However, for analyses which ended up with an error (e.g. "Unable to align") this column was mistakenly missing. In this version we fix this omission.

Fix gene map width in Nextclade Web

Gene map (genome annotation) was misaligned with sequence views (not matching their width). This has been fixed in this version.

Add table row indices to results table in Nextclade Web

We added a column with index of the row in the table. This is useful for visual search and counting of sorted and filtered results.

Not to be confused with sequence index. Row indices always start with 0 and sorted in ascending order, and do not change their position when sorting or filtering the results.

These indices are not a part of output files. Nextclade CLI is not affected.

Improve error messages

Errors due to failure of sequence alignment are reworded and hopefully are more complete and comprehensible now. Additionally, we improved error message when reference sequence fails to read.

Always show action buttons on results page in Nextclade Web

On smaller screens the "Download", "Tree" and other action buttons were not visible by default and horizontal scrolling were required to see them. We changed the layout such that the panel with buttons does not overflow along with table and so the buttons are always visible. Table is still scrollable.

Improve wording on main page of Nextclade Web

We improved text on main page as well as descriptions inside HTML markup, adding more concrete information and keywords. This should be more pleasant to read and might improve Nextclade ranking in search engines.

Commit history

(click to expand)

Instructions

📥 Nextclade CLI & Nextalign CLI can be downloaded from the links in the "Assets" section just below. There click "Show all" to show more options. Note the difference between "nextalign" and "nextclade" files.

🌐 Nextclade Web is available at https://clades.nextstrain.org

🐋 Docker images are available at DockerHub

📚 To understand how it all works, make sure to read the Documentation

Scientific Software - Peer-reviewed - Rust
Published by nextstrain-bot about 3 years ago

Nextclade - 2.10.1

Nextclade CLI 2.10.1 (2023-01-24)

Ensure `--output-all`, `--output-tsv`, `--output-csv` can be used together again in Nextclade CLI

This fixes a regression introduced in Nextclade CLI 2.10.0, where --output-all, --output-tsv, --output-csv arguments became mutually exclusive. This was not intended and now resolved.

This bug was breaking our bioconda checks, so Nextclade CLI version 2.10.0 will not be available in bioconda. Use 2.10.1 instead.

Nextclade Web is not affected.

Commit history

(click to expand)

Instructions

📥 Nextclade CLI & Nextalign CLI can be downloaded from the links in the "Assets" section just below. There click "Show all" to show more options. Note the difference between "nextalign" and "nextclade" files.

🌐 Nextclade Web is available at https://clades.nextstrain.org

🐋 Docker images are available at DockerHub

📚 To understand how it all works, make sure to read the Documentation

Scientific Software - Peer-reviewed - Rust
Published by nextstrain-bot about 3 years ago

Nextclade - 2.10.0

Nextclade Web 2.10.0, Nextclade CLI 2.10.0 (2023-01-24)

Add motifs search

Nextclade datasets can now be configured to search for motifs in the translated sequences, given a regular expression.

At the same time, we released new versions of the following Influenza datasets, which use this feature to detect glycosylation motifs:

Influenza A H1N1pdm HA (fluh1n1pdmha), with reference MW626062
Influenza A H3N2 HA (fluh3n2ha), with reference EPI1857216

If you run the analysis with the latest version of these datasets, you can find the results in the glycosylaiton column or field of output files or in "Glyc." column in Nextclade Web.

If you want to configure your own datasets for motifs search, see an example configuration in the aaMotifs property of virus_properties.json of these datasets: link.

Allow to chose columns written into CSV and TSV outputs

You can now select a subset of columns to be included into CSV and TSV output files of Nextclade Web (available in the "Download" dialog) and Nextclade CLI (available with --output-csv and --output-tsv). You can either chose individual columns or categories of related columns.

In Nextclade Web, in the "Download" dialog, click "Configure columns", then check or uncheck columns or categories you want to keep. Note that this configuration persists across different Nextclade runs.

In Nextclade CLI, use --output-columns-selection flag. This flag accepts a comma-separated list of column names and/or column category names. Individual columns and categories can be mixed together. You can find a list of column names in the full output file. The following categories are currently available: all, general, ref-muts, priv-muts, errs-warns, qc, primers, dynamic. Another way to receive both lists is to add a non-existent or misspelled name to the list. The error message will then display all possible columns and categories.

Note that because of this feature the order of columns might be different compared to previous versions of Nextclade.

Add URL parameter for running analysis of example sequences

You can now launch the analysis of example sequences (as provided by the dataset) in Nextclade Web, by using the special keyword example in the input-fasta URL parameter. For example, navigating to this URL will run the analysis of example SARS-CoV-2 sequences (same as choosing "SARS-CoV-2" and then clicking "Load example" in the UI):

https://clades.nextstrain.org/?dataset-name=sars-cov-2&input-fasta=example

This could useful for example for testing new datasets:

https://clades.nextstrain.org/?dataset-url=http://example.com/my-dataset-dir&input-fasta=example

Add `index` column to CSV and TSV outputs

The index field is already present in other output formats. In this version CSV and TSV output files gain index column as well, which contains the index (integer signifying location) of a corresponding record in the input fasta file or files. Note that this is not the same as row index, because CSV/TSV rows can be emitted in an unspecified order in Nextclade CLI (but this can be changed with --in-order flag; which is set by default in Nextclade Web).

Note that sequence names (seqName column) are not guaranteed to be unique (and in practice are not unique very often). So indices is the only way to reliably link together inputs and outputs.

Scientific Software - Peer-reviewed - Rust
Published by nextstrain-bot about 3 years ago

Nextclade - 2.9.1

Nextclade Web 2.9.1, Nextclade CLI 2.9.1 (2022-12-09)

Set default weights in "private mutations" QC check to 1

This fixes the bug when the QC score is 0 (good) when the following QC fields are missing from qc.json:

.privateMutations.weightLabeledSubstitutions .privateMutations.weightReversionSubstitutions .privateMutations.weightUnlabeledSubstitutions

In this case Nextclade assumed value of 0, which lead to QC score of 0 always. Not all datasets were adjusted for the new qc.json format in time and some had these fields missing - notably the flu datasets. So these datasets were erroneously showing perfect QC score for the "private mutations" rule.

In this version we set these weights to 1.0 if they are missing, which fixes the incorrect QC scores. Some of the sequences will now correctly show worse QC scores.

Fix dataset selector in Nextclade Web when there are datasets with the same name, but different reference sequences

The dataset selector on the main page on nextclade Web did not allow selecting datasets with the same name, but different reference sequences. This did not affect users so far, but we are about to release new Influenza datasets, which were affected. In this version we resolve the problem by keeping track of datasets not just by name, but by a combination of all attribute values (the .attributes[] entries in the datasets index JSON file).

Ensure non-default references in "dataset list" command of Nextclade CLI are shown

This introduces special value all for --reference argument of nextclade dataset list command. And it is now set as default. When it's in force, datasets with all reference sequences are included into the displayed list. This resolves the problem where non-default references are not show in the list.

Internal changes

We are now submitting PRs to bioconda automatically, which should reduce the delay of updates there

Commit history

(click to expand)

Instructions

📥 Nextclade CLI & Nextalign CLI can be downloaded from the links in the "Assets" section just below. There click "Show all" to show more options. Note the difference between "nextalign" and "nextclade" files.

🌐 Nextclade Web is available at https://clades.nextstrain.org

🐋 Docker images are available at DockerHub

📚 To understand how it all works, make sure to read the Documentation

Scientific Software - Peer-reviewed - Rust
Published by github-actions[bot] about 3 years ago

Nextclade - 2.9.0

Nextclade Web 2.9.0, Nextclade CLI 2.9.0 (2022-12-06)

Increase requirements for supported Linux distributions for GNU flavor of Nextclade CLI

Due to malfunction of package repositories of Debian 7, we had to switch automated builds of the "gnu" flavor of Nextclade CLI from Debian 7 to CentOS 7. This increases minimum required version of glibc to 2.17. The list or Linux distributions we tested the new version of Nextclade on is here. For users of older Linux distributions (with glibc < 2.17) we suggest to use "musl" flavor of Nextclade CLI, which does not depend on glibc, but might be substantially slower. Users of Nextclade CLI on macOS and Windows and users of Nextclade Web are not affected.

Add gene length validation in GFF3 parser

Nextclade will now check if genes have length divisible by 3 in gene maps and will fail with an error if it's not the case.

Fix translated (internationalized) strings in Nextclade Web

We fixed missing spaces between words in some of the languages and fixes some of the translations.

Internal changes

build Linux binaries on CentOS 7
migrate CI to GitHub Actions
upgrade Rust to 1.65.0

Commit history

(click to expand)

Instructions

📥 Nextclade CLI & Nextalign CLI can be downloaded from the links in the "Assets" section just below. There click "Show all" to show more options. Note the difference between "nextalign" and "nextclade" files.

🌐 Nextclade Web is available at https://clades.nextstrain.org

🐋 Docker images are available at DockerHub

📚 To understand how it all works, make sure to read the Documentation

Scientific Software - Peer-reviewed - Rust
Published by nextstrain-bot about 3 years ago

Nextclade - 2.8.0

Nextclade Web 2.8.0, Nextclade CLI 2.8.0 (2022-10-20)

Community datasets in Nextclade Web

This release adds support for fetching custom datasets from a remote location. This can be used for testing datasets introducing support for new pathogens, as well as for sharing these datasets with the community.

For that, we added the dataset-url URL query parameter, where you can specify either a direct URL to the directory of your custom dataset:

https://clades.nextstrain.org?dataset-url=http://example.com/path/to/dataset-dir

or a URL to a GitHub repository:

https://clades.nextstrain.org?dataset-url=https://github.com/my-name/my-repo/tree/my-branch/path/to/dataset-dir

or a special shortcut to a GitHub repository:

https://clades.nextstrain.org?dataset-url=github:my-name/my-repo@my-branch@/path/to/dataset-dir

If a branch name is not specified, the default branch name is queried from GitHub. If a path is omitted, then the files are fetched from the root of the repository.

When dataset-url parameter is specified, instead of loading a list of default datasets, a single custom dataset is loaded from the provided address. Note that this should be publicly accessible and have CORS enabled. GitHub public repositories already comply with these requirements, so if you are using a GitHub URL or a shortcut, then no additional action is needed.

For more information, refer to: - PR #1026 - Nextclade documentation on datasets - Nextclade data repo - Nextclade developers guide

Compression of all input and output files in Nextclade CLI and Nextalign CLI

Previously, only FASTA files could be compressed and decompressed on the fly. Now Nextclade CLI and Nextalign CLI can read all input and write all output files in compressed formats. Simply add one of the supported file extensions: "gz", "bz2", "xz", "zstd", and the files will be compressed or decompressed transparently.

Decrease default number of threads in Nextclade Web

Some users have observed long startup times of the analysis in Nextclade Web. In this release we decreased the default number of processing threads from 8 to 3, such that startup time is now a little faster.

If you want to speedup the analysis of large batches of sequences, at the expense of longer startup time, you can tune the number of threads in the "Settings" dialog.

Improve readability of text fragments in Nextclade Web

We've made text paragraphs on main page and some other places a little prettier and hopefully more readable.

Fix crash when reading large, highly-nested tree files

We improved handling of Auspice JSON format, such that it no longer crashes when large trees and trees with large number of deep branches are provided.

Commit history

(click to expand)

- [[`7438805`](https://github.com/nextstrain/nextclade/commit/7438805b5254fec90c45fecbddb83fe9eda85107)] chore(deps): bump auspice in /packages_rs/nextclade-web Bumps [auspice](https://github.com/nextstrain/auspice) from 2.38.0 to 2.39.0. - [Release notes](https://github.com/nextstrain/auspice/releases) - [Changelog](https://github.com/nextstrain/auspice/blob/master/CHANGELOG.md) - [Commits](https://github.com/nextstrain/auspice/compare/v2.38.0...v2.39.0) --- updated-dependencies: - dependency-name: auspice dependency-type: direct:production update-type: version-update:semver-minor ... Signed-off-by: dependabot[bot] - [[`891af32`](https://github.com/nextstrain/nextclade/commit/891af32ab1da481e6107158de09311218777fd1e)] Update clades.svg - [[`0e41219`](https://github.com/nextstrain/nextclade/commit/0e4121918b2f02fe82567ce92e9c2ecb7a664e2f)] Merge pull request #1013 from nextstrain/update-clades-svg Update clades.svg - [[`77bcc03`](https://github.com/nextstrain/nextclade/commit/77bcc03b2df3b1892e241ee09c8bd9802f719d0e)] Merge pull request #1012 from nextstrain/dependabot/npm_and_yarn/packages_rs/nextclade-web/auspice-2.39.0 - [[`e6aab13`](https://github.com/nextstrain/nextclade/commit/e6aab13f39777d36355207a92a5b6e9a5ddff0e7)] chore: release web v2.7.1 - [[`3de3205`](https://github.com/nextstrain/nextclade/commit/3de3205a283258fbf3e3934d9e340d2e49b0c016)] chore: disable core dumps when running dev docker container [skip ci] - [[`6cb95a4`](https://github.com/nextstrain/nextclade/commit/6cb95a4c12c95d34dce8f9d8c1bd4dce5b6b1759)] refactor: minify clades.svg - [[`02ea73a`](https://github.com/nextstrain/nextclade/commit/02ea73a066e40d031235e2a1400e0c9a67e61d29)] feat(web): prettify markdown rendering, changelog window text Applies small visual fixes and tweaks to make markdown text a little more readable. Highlights headings in the changelog and fixes a few visual bugs in code snippets. Removes unnecessary and unused styles. - [[`63f6d21`](https://github.com/nextstrain/nextclade/commit/63f6d21324d2f488c8849e951d1f5780e6eb8386)] Merge pull request #1016 from nextstrain/refactor/web-minify-clades-svg - [[`82b93f2`](https://github.com/nextstrain/nextclade/commit/82b93f2f1ddc8bc033ecc30c162402f90dc35f6a)] Merge pull request #1017 from nextstrain/feat/web-prettier-markdown - [[`2539c25`](https://github.com/nextstrain/nextclade/commit/2539c25c0a91e1d21e59fa8ef33ba8b61d9a6cf6)] fix: ensure parsing of large, highly-nested tree JSONs Resolves https://github.com/nextstrain/nextclade/issues/1018 When tree JSON is sufficiently nested, `serde_json` fails to parse it into the `AuspiceTree` `struct` with: ``` recursion limit exceeded at line column ``` This problem has been reported before in `serde_json` in https://github.com/serde-rs/json/issues/334, and the solution allowing to remove the recursion limit was implemented in the form of [`Deserializer::disable_recursion_limit`](https://docs.rs/serde_json/latest/serde_json/struct.Deserializer.html#method.disable_recursion_limit) traded off to the increased risk of overflowing the call stack. So here I implemented the suggested solution, by calling the `disable_recursion_limit()` on deserializer. I am also mitigating the risk of stack overflow by using growing stack adapter from [`serde_stacker`](https://docs.rs/serde_stacker/latest/serde_stacker/). This allows to successfully parse the large tree from https://github.com/nextstrain/nextclade/issues/1018, although probably also makes the tree parsing a bit slower. But it is not critical for overall runtime, as it is a one-off operation. - [[`7c437b0`](https://github.com/nextstrain/nextclade/commit/7c437b0ab17587235ec1bc5bc8efa11f03771267)] chore: remove unrelated changes [skip ci] - [[`6ed348b`](https://github.com/nextstrain/nextclade/commit/6ed348b6ff2ecaa11f3424b8472f6845379a30ef)] refactor: deduplicate json parsing code - [[`33fd032`](https://github.com/nextstrain/nextclade/commit/33fd03274832846293d0578ba4b2cbb98489e5b6)] feat(web): dynamically set dataset server root using a URL param Allows to dynamically set dataset server root URL in Nextclade Web on runtime. It is sufficient to add URL parameter `dataset-server` with the value containing URL to the root of the dataset file server (containing `index_v2.json`), and Nextclade Web will fetch dataset index and all dataset files from this server instead of the default: ``` ?dataset-server=http://example.com ``` The localhost URLs should also work: ``` ?dataset-server=http://localhost:27722 ``` This is equivalent to `--server` flag in Nextclade CLI. This should facilitate testing of custom datasets in Nextclade Web. - [[`02b19a2`](https://github.com/nextstrain/nextclade/commit/02b19a256cdbc37c66bc856aa74f9800b80efd22)] chore: enable CORS for local dataset server - [[`064393e`](https://github.com/nextstrain/nextclade/commit/064393ea6fabd713d201b383d69c2093fc63aa2b)] docs: document dataset-server URL param - [[`ed4b775`](https://github.com/nextstrain/nextclade/commit/ed4b775da1bfe26d30b501590d5837d42b56d8b8)] feat(web): reduce default number of threads to speedup initialization Despite "thread" (actually webworker) initialization is supposed to be concurrent, there seem to be a clear trend of increased initialization time as number of threads increased. This is likely due to data transfer overhead between workers. Here I reduce number of threads that can be initialized with default settings. But these setting can always be altered in the "Settings" dialog. - [[`c4e7736`](https://github.com/nextstrain/nextclade/commit/c4e77367ec3a742f818299a7447ef3e57e282d83)] Merge pull request #1020 from nextstrain/feat/web-dataset-server-url-param - [[`7890180`](https://github.com/nextstrain/nextclade/commit/78901802745f3a18926337779aeb2a2a08341cde)] Merge branch 'master' into fix/tree-json-parsing-recursion-limit - [[`ecdff00`](https://github.com/nextstrain/nextclade/commit/ecdff0041fab4b9a77046e5c24ae6278e239b026)] Merge pull request #1021 from nextstrain/feat/web-decrease-num-threads - [[`d677b95`](https://github.com/nextstrain/nextclade/commit/d677b950dc85e21bd5a4c10ebed664fc67a24a71)] docs: add info about dataset-server URL param to dev guide [skip ci] - [[`e77141e`](https://github.com/nextstrain/nextclade/commit/e77141e115a672fd5688fe89ba8a566585b4648f)] Merge remote-tracking branch 'origin/master' into fix/tree-json-parsing-recursion-limit - [[`62008ff`](https://github.com/nextstrain/nextclade/commit/62008ff877b6378e5e8a5ca06200d2044e96da40)] feat: improve file io logic - [[`ddef52d`](https://github.com/nextstrain/nextclade/commit/ddef52d7707598e8f9a452127bc353ca932e3794)] feat(web): fetch custom dataset from github - [[`68bf7b8`](https://github.com/nextstrain/nextclade/commit/68bf7b8fd62f09eff6a2c0b4ee36bd2dbdb4a159)] feat(web): check existence of github dataset files, use tag data - [[`ed20825`](https://github.com/nextstrain/nextclade/commit/ed208252c6b3e80121d17a5bee410eef860401c0)] refactor: lint - [[`f0c460a`](https://github.com/nextstrain/nextclade/commit/f0c460a309c657fa762163580b5cd8ed4e7f7db2)] feat: ensure github urls to the root of a repo also work - [[`a79a6df`](https://github.com/nextstrain/nextclade/commit/a79a6df0022b22608219dfaa6e63e487590bf801)] refactor: split github function into a separate module - [[`cb6b6c1`](https://github.com/nextstrain/nextclade/commit/cb6b6c1d66b991905edb5a06c85503f3cb29fe6f)] refactor: treat dataset attributes as optional in tag.json - [[`c76e5dd`](https://github.com/nextstrain/nextclade/commit/c76e5ddcda979fd82755865c31d347b673ae531a)] feat(web): accept shortcut GitHub URLs Allows `?dataset-github=` URL param to accept shortcuts instead of full URLs for GitHub repos: ``` github:owner/org github:owner/org/path/to/file github:owner/org@branch@ github:owner/org@branch@/path/to/file ``` If a branch is not specified, the default branch is queried from GitHub REST API (subject to rate limits). Example: ``` ?dataset-github=github:nextstrain/nextclade_data@master@/data/datasets/flu_yam_ha/references/JN993010/versions/2022-07-27T12:00:00Z/files ``` - [[`144c6b4`](https://github.com/nextstrain/nextclade/commit/144c6b461044a503e175dd97b7c42de91224b940)] feat: make `sequences.fasta` optional - [[`6124f64`](https://github.com/nextstrain/nextclade/commit/6124f64f08220886d73f8a4977634e47d1d5a561)] feat(web): allow shorter prefix in github shortcuts Let's allow a shorter `gh:` prefix additionally to `github:` in shortcut GitHub URLs - [[`3858008`](https://github.com/nextstrain/nextclade/commit/3858008fa650b39d4c49317d408d8fec029ce3c8)] feat(web): remove `dataset-github`, detect `dataset-url` type automatically Let's have only one URL param and detect whether we need to treat special cases (GitHub) based on the value. - [[`6cd8f2e`](https://github.com/nextstrain/nextclade/commit/6cd8f2eee9b904b21d22849cc46ca99ea740bede)] fix: replace example GitHub url with a permalink - [[`d747e62`](https://github.com/nextstrain/nextclade/commit/d747e6295a8598c0babc34a98cc6d1a74e0522cc)] docs: document the new dataset-url URL param [skip ci] - [[`f5dfc40`](https://github.com/nextstrain/nextclade/commit/f5dfc4040d9fcc8b273746164c780ccfd18676b3)] Merge pull request #1026 from nextstrain/feat/datasets-from-github - [[`9913aef`](https://github.com/nextstrain/nextclade/commit/9913aef05f439545f360620d5dccf8b7194c31a6)] Merge pull request #1019 from nextstrain/fix/tree-json-parsing-recursion-limit - [[`f3591eb`](https://github.com/nextstrain/nextclade/commit/f3591ebbfae66268d502f8c808f203dd636e0899)] perf: remove mimalloc It was not configured correctly, due to mistake in `cfg` conditional and even when set up correctly does not make Nextclade any faster. See: https://github.com/nextstrain/nextclade/issues/1027 - [[`15fe4af`](https://github.com/nextstrain/nextclade/commit/15fe4af14d2ddabad36b52dd81c3671d718a03b0)] Merge pull request #1028 from nextstrain/perf/allocator-default - [[`6ee3450`](https://github.com/nextstrain/nextclade/commit/6ee34504c84f5bbefeb6675be4616053201c3a9a)] Merge remote-tracking branch 'origin/master' into feat/better-file-io - [[`338c0dc`](https://github.com/nextstrain/nextclade/commit/338c0dc268effb5163daf4aa24c28f983ee9fb42)] refactor: clarify function names, extract constant - [[`20fecc1`](https://github.com/nextstrain/nextclade/commit/20fecc16c45fc11f8caecf7ecbc7840ad3a2598f)] Merge pull request #1029 from nextstrain/feat/better-file-io - [[`a7610d5`](https://github.com/nextstrain/nextclade/commit/a7610d50338faa0026a2ab6d4227400d0cb7be93)] feat(cli): add info about compression to cli help Followup of https://github.com/nextstrain/nextclade/pull/1029 Extends CLI help, now that we can read and write any file in compressed formats. - [[`f4f54c0`](https://github.com/nextstrain/nextclade/commit/f4f54c0fd7273c7fd4bfc55b9f6140490c20ddc9)] Merge pull request #1030 from nextstrain/feat/cli-help-file-io - [[`e73f4a1`](https://github.com/nextstrain/nextclade/commit/e73f4a1ee8d321d1cf95a58aa1200c1539b476d5)] fet(web): increase spacing between headings in changelog - [[`4c82d30`](https://github.com/nextstrain/nextclade/commit/4c82d30462a31954b01bcf701919ed57af335f48)] Merge pull request #1031 from nextstrain/feat/web-md-headings - [[`ba80d9f`](https://github.com/nextstrain/nextclade/commit/ba80d9f39e9cf4c5bee579cc756024a4da84a535)] chore: release web and cli 2.8.0

Instructions

📥 Nextclade CLI & Nextalign CLI can be downloaded from the links in the "Assets" section just below. There click "Show all" to show more options. Note the difference between "nextalign" and "nextclade" files.

🌐 Nextclade Web is available at https://clades.nextstrain.org

🐋 Docker images are available at DockerHub

📚 To understand how it all works, make sure to read the documentation

Scientific Software - Peer-reviewed - Rust
Published by nextstrain-bot over 3 years ago

Nextclade - 2.7.0

Nextclade CLI 2.7.0, Nextclade Web 2.7.0 (2022-10-05)

Hide custom clade columns

We added ability to mark certain custom clade columns as hidden. In this case they are not shown in Nextclade Web. This prepares the web application for the upcoming reorganization of clade columns. It should not affect current users.

Remove unused fields from output files, add custom phenotype key list

We removed extra repetitive fields related to custom phenotype columns (e.g. "Immune escape" and "ACE-2 binding") from JSON and NDJSON output files. We also added keys for custom phenotype columns to the header section of output JSON, for symmetry with custom clade columns. These changes should not affect most users.

Commit history

(click to expand)

- [[`21c5e5e`](https://github.com/nextstrain/nextclade/commit/21c5e5ef3d760c4dd7933dca05830bc665540f77)] chore: apply automatic clippy lint fixes - [[`d71864c`](https://github.com/nextstrain/nextclade/commit/d71864ce54bf7e14501618022b3626870f187814)] chore: lint - [[`de4079a`](https://github.com/nextstrain/nextclade/commit/de4079ad798321a9204cdbc6879819408aaa68ff)] chore: format - [[`296e9f8`](https://github.com/nextstrain/nextclade/commit/296e9f8a3ae10e5ba553a243d6aed8a9e848eb9d)] Merge pull request #1003 from nextstrain/chore/lint - [[`362f280`](https://github.com/nextstrain/nextclade/commit/362f280e687d1d09680891aa45183502fe62b217)] chore(ci): only release cli from release-cli branch - [[`8337dc0`](https://github.com/nextstrain/nextclade/commit/8337dc099467fc4c26cdd8a732972bd1f8830c4d)] fix: link to release dataset changlog Currently release users see master dataset changelog. Here I change the link such that they see dataset changelog on release branch, i.e. only released dataset changes. - [[`95bda16`](https://github.com/nextstrain/nextclade/commit/95bda160675cbdacdde4c88d07db6fbe8b13f19a)] Merge pull request #1004 from nextstrain/fix/web-dataset-changelog-link - [[`ccb35e9`](https://github.com/nextstrain/nextclade/commit/ccb35e97d43eecbbf666c0f32e43e08bdb0deb70)] feat(web): format tooltip text Format text of custom phenotype columns. This text comes from a JSON string, so formatting capabilities are very limited. Here I split the incoming string on `\n` and create paragraphs (`

`) from each fragment. - [[`6f48b17`](https://github.com/nextstrain/nextclade/commit/6f48b175495097fecf5f08a79b8479f41a3115d2)] Merge pull request #1005 from nextstrain/feat/web-format-tooltip-text - [[`f7d3ae8`](https://github.com/nextstrain/nextclade/commit/f7d3ae85d20719c3a0675aa461f51da9bbc43aeb)] chore: release web v2.6.1 - [[`7f6cd6b`](https://github.com/nextstrain/nextclade/commit/7f6cd6bdc1cf5dd70491ef36496f549a195a2009)] feat: allow hiding custom clade columns - [[`8e7eb64`](https://github.com/nextstrain/nextclade/commit/8e7eb6468099a40ebba11f190cc7c4083f70b6de)] fix: show custom clade columns by default Let's flip the boolean, so that it's natural default is `false` - [[`54117cf`](https://github.com/nextstrain/nextclade/commit/54117cf874a501233de65f136747d7c62718f276)] fix: remove unused data from outputs Removes `results[].phenotypeValues.nameFriendly` and `results[].phenotypeValues.description` from output JSON and NDJSON. These fields were not intended to be used, are repeated and increase file size needlessly. - [[`ee0c659`](https://github.com/nextstrain/nextclade/commit/ee0c659d3df32c226dd1cefc6d738bebf831f499)] fix: add descriptions for phenotype attributes to outputs Adds descriptions of phenotype attributes to `.phenotypeAttrKeys` of JSON output. This is for symmetry with the similarly implemented `.cladeNodeAttrKeys` attributes. - [[`f145b45`](https://github.com/nextstrain/nextclade/commit/f145b45eae843a5489378058b220c7f0dd673c90)] Merge pull request #1009 from nextstrain/fix/remove-unused-output-data - [[`c8fe93e`](https://github.com/nextstrain/nextclade/commit/c8fe93ef9ddc7e887a6dddaa41590c74df8c4f9c)] Merge pull request #1010 from nextstrain/fix/add-phenotype-descriptions-to-outputs - [[`d30d608`](https://github.com/nextstrain/nextclade/commit/d30d60885f8a68d382b04570f388cdeb094503aa)] fix: reset node attr state correctly across runs - [[`ade06e2`](https://github.com/nextstrain/nextclade/commit/ade06e267f3ab54976caff792f414368c9fd7f2a)] Merge pull request #1006 from nextstrain/feat/allow-hiding-custom-clade-columns feat: allow hiding custom clade columns - [[`1c3377b`](https://github.com/nextstrain/nextclade/commit/1c3377b22b43acb5b7231300897d29636b78dd02)] chore: speedup wasm dev build Here for wasm dev build I replace the `wasm-pack` which is nice, but behind its defaults it hides lots of useful stuff, and I call `cargo build`, `wasm-bindgen` and `wasm-opt` explicitly. Notably `wasm-pack` does not allow custom cargo profiles (https://github.com/rustwasm/wasm-pack/issues/1111). I also add the new "opt-dev" cargo profile, which is something in the middle between `release` and `dev` - a balance between rebuild speed and runtime performance. This should save lots of time during day-to-day work. The production version still uses `wasm-pack` and a more tried solution. The dev version now requires cargo wasm toolchain, `wasm-bindgen` and `wasm-opt` (from `binaryen` project) installed manually. Previously `wasm-pack` would handle that. The dev docker image was updated accordingly. - [[`ae49768`](https://github.com/nextstrain/nextclade/commit/ae497682278c2319fa5013e35479359d4a8a5dc8)] fix: adjust import For the changes in 1c3377b22b43acb5b7231300897d29636b78dd02 (there no longer is `package.json`, so import of the directory does not work) - [[`4f5db09`](https://github.com/nextstrain/nextclade/commit/4f5db091285a390bccc966283aafa78b61e7d21e)] fix(web): crash when exporting files in web Followup of https://github.com/nextstrain/nextclade/pull/1006 The PR https://github.com/nextstrain/nextclade/pull/1006 introduced a bug: it filters away hidden columns from recoil state, thus making them unavailable for export functions. The mismatch in expected columns caused crash on Rust side. Here I modify the filtering logic, moving it to the actual rendering site, instead of filtering globally. This way, hidden columns are not rendered, but are still be available for export. - [[`f0975a2`](https://github.com/nextstrain/nextclade/commit/f0975a2914b6f073dd1a3314c9006e5bab7463ef)] chore: remove unused script [skip ci] - [[`19b1932`](https://github.com/nextstrain/nextclade/commit/19b1932d2cd252e85745e0e3fac3bc83121e0669)] chore: document dev scripts [skip ci] - [[`70122ce`](https://github.com/nextstrain/nextclade/commit/70122ce5c018718cd36f008ca26dbbb6c76e5147)] Merge pull request #1011 from nextstrain/fix/web-crash-on-export - [[`66c6dd2`](https://github.com/nextstrain/nextclade/commit/66c6dd25b01a762afe915c2f349c9a876b0d53ea)] chore: release web and cli 2.7.0

Scientific Software - Peer-reviewed - Rust
Published by nextstrain-bot over 3 years ago

Nextclade - 2.6.0

Nextclade Web 2.6.0, Nextclade CLI 2.6.0 (2022-09-27)

New metrics: Immune escape and ACE-2 binding

We added software support for the new custom metrics in Nextclade CLI and nextclade Web. The dataset "sars-cov-2-21L" with the data required for these metrics to appear will be released in the coming days. Stay tuned.

The `dataset-name` URL parameter is now properly applied in Nextclade Web, even when `input-fasta` is not provided

Previously dataset-name URL parameter was ignored, unless input-fasta is also set. Now the dataset-name will make Nextclade Web to preselect the requested dataset, regardless of whether the input-fasta URL parameter is also provided. This allows to create URLs which preconfigure Nextclade Web with a certain dataset and dataset customizations, with intent to provide fasta and to run manually.

Better error handling

We improved error handling, such that some of the errors in Nextclade Web now have better error messages. Some of the errors that previously caused hard crash in in Nextclade CLI are now handled more gracefully and with better error messages.

Internal changes

We upgraded Rust to 1.63.0 and Nextclade CLI and Nextalign CLI are now using std::thread::scope for better multithreading support.

Commit history

(click to expand)

- [[`b2ba122`](https://github.com/nextstrain/nextclade/commit/b2ba1224ce4ef89977da9223314fb1061ecce1c3)] chore: remove deprecation notices from v1 - [[`3a374c2`](https://github.com/nextstrain/nextclade/commit/3a374c2a641fac3531a053a76504d4a9e454ef6c)] refactor: move types.ts file It is lonely in the old deprecated `algorithms/` directory, let's put it at the root. Remaining changes are just import path change (automated). - [[`0583e91`](https://github.com/nextstrain/nextclade/commit/0583e91e99c38e4a05abf54bb3b41ecbfe09a5c8)] refactor: format - [[`4a17d36`](https://github.com/nextstrain/nextclade/commit/4a17d36cad60c2d9b4ea8f78171d04ac2ea0872d)] Merge pull request #981 from nextstrain/refactor/cleanup - [[`ab12755`](https://github.com/nextstrain/nextclade/commit/ab1275561d4235b0b2f737e4014b57ac1711d047)] fix(web): correct text instructions for fasta text fields - [[`129f549`](https://github.com/nextstrain/nextclade/commit/129f549b454f6c95b60ccb3d22161023814b3d6f)] Merge pull request #983 from nextstrain/fix/text-field-text - [[`7ea8414`](https://github.com/nextstrain/nextclade/commit/7ea8414fc67e6bf1a28b0b6d31404e8ac0504f8e)] fix: consider different file encodings This attempts to mitigate crash in web when the fasta file is not UTF-8 or ASCII encoded. Here I am trying to deduce a list of encodings the file resembles and then attempting to decode the contents of the file from these encodings to a JS string, instead of simply using the `FileReader`'s `.toString()` function. - [[`992fc57`](https://github.com/nextstrain/nextclade/commit/992fc579a2c409c100957b157aea06340bd25987)] refactor: lint - [[`6f4b5b4`](https://github.com/nextstrain/nextclade/commit/6f4b5b4ed236c92fc39dcac0d6c6f4f535e6ffab)] feat: try a more accurate chardet library - [[`b0f7bf2`](https://github.com/nextstrain/nextclade/commit/b0f7bf25215850c3d1ead0433df1e9ba00e683d7)] feat: rephrase error message - [[`18d8716`](https://github.com/nextstrain/nextclade/commit/18d87161670f5ae5cd1e9dfc7682d567350015de)] Merge pull request #987 from nextstrain/fix/web-file-encoding - [[`f6bdaae`](https://github.com/nextstrain/nextclade/commit/f6bdaae32b374e7986fa1340c5c085bdf9792409)] refactor: lint, fix typings - [[`86e2ac1`](https://github.com/nextstrain/nextclade/commit/86e2ac130d079fd6e6854911fd33c1ae8347d3e4)] Merge pull request #988 from nextstrain/refactor/lint - [[`e8cce45`](https://github.com/nextstrain/nextclade/commit/e8cce457e2aaafac7d8dc4f158ccbe054e07a9ee)] feat: calculate escape - [[`b5c6b29`](https://github.com/nextstrain/nextclade/commit/b5c6b296f2986a62441d46bf826ab17f2766fbf7)] feat: add escape to csv and tsv outputs - [[`add2a85`](https://github.com/nextstrain/nextclade/commit/add2a855243de790a4e70587d11c4aa78e0f908f)] feat(web): add escape column - [[`551e4e2`](https://github.com/nextstrain/nextclade/commit/551e4e22886411c283a914ebc96be506fa3af687)] feat: hide 'Escape' column when there aren't any values - [[`e4c02b0`](https://github.com/nextstrain/nextclade/commit/e4c02b0f62a1cc8f630f2cd2a627c4360328aea7)] refactor: lint - [[`8694a52`](https://github.com/nextstrain/nextclade/commit/8694a52640fa48a6570414a3dd5274b7e46e4f75)] feat: avoid sending filenames to plausible - [[`f5cbfa2`](https://github.com/nextstrain/nextclade/commit/f5cbfa201557630a1dca7228534b5a56d989f795)] feat: improve error page and popup - [[`b2f3b41`](https://github.com/nextstrain/nextclade/commit/b2f3b417cc62ff818c125e1300df8d09206c46aa)] refactor: lint - [[`9650e27`](https://github.com/nextstrain/nextclade/commit/9650e27c2dc4472f858b50ae767f31ecc4ffed9c)] Merge pull request #992 from nextstrain/feat/web-improve-error-handling - [[`ccbcacf`](https://github.com/nextstrain/nextclade/commit/ccbcacfb1dc1c8321c25fc62603be6e0b7f2dafa)] feat: extract translation strings - [[`ff265c1`](https://github.com/nextstrain/nextclade/commit/ff265c1aefa00b361cdf69603ae4adb0bd64deb0)] Merge branch 'feat/extract-translation-strings' - [[`628666a`](https://github.com/nextstrain/nextclade/commit/628666a927cca2b1ba5124089f53a19dffc8ff74)] feat: setup automatic translation with AWS Translate - [[`d4e9bde`](https://github.com/nextstrain/nextclade/commit/d4e9bde681e483ce65eb0cf246cf05e008e37602)] Merge pull request #993 from nextstrain/feat/autotranslate - [[`a674e35`](https://github.com/nextstrain/nextclade/commit/a674e358ef2722c187ef876c41972222ec7fc824)] feat: apply automatic translations - [[`b7a3ab1`](https://github.com/nextstrain/nextclade/commit/b7a3ab1acd86f4a3955eb5377ac2453af43ba4e5)] feat(web): add more languages - [[`14b98fc`](https://github.com/nextstrain/nextclade/commit/14b98fc872ea7af7d1e3dfdffd09575f4ad41814)] feat(web): translate more strings - [[`31bc2ef`](https://github.com/nextstrain/nextclade/commit/31bc2ef8d19bbf4a182d21a96f6292db823630ea)] refactor: correct compiler error - [[`b495e7b`](https://github.com/nextstrain/nextclade/commit/b495e7b1c5ea8e9124ace0ae3474f03231306ec9)] feat(web): persist selected locale - [[`e9f63e1`](https://github.com/nextstrain/nextclade/commit/e9f63e1d215f0f59bb3a618f87725474d4a58049)] fix(web): sort locales - [[`f90856b`](https://github.com/nextstrain/nextclade/commit/f90856b417dddffadd2190497b246158777e8e45)] Merge pull request #994 from nextstrain/feat/translate - [[`09ec70c`](https://github.com/nextstrain/nextclade/commit/09ec70c6e72eb90b0edf084067311a08e66cd1ac)] chore(deps): bump auspice in /packages_rs/nextclade-web Bumps [auspice](https://github.com/nextstrain/auspice) from 2.37.3 to 2.38.0. - [Release notes](https://github.com/nextstrain/auspice/releases) - [Changelog](https://github.com/nextstrain/auspice/blob/master/CHANGELOG.md) - [Commits](https://github.com/nextstrain/auspice/compare/v2.37.3...v2.38.0) --- updated-dependencies: - dependency-name: auspice dependency-type: direct:production update-type: version-update:semver-minor ... Signed-off-by: dependabot[bot] - [[`d3b35c3`](https://github.com/nextstrain/nextclade/commit/d3b35c36aa182a7a932648bc1d6c3f0de4cb58a2)] Merge pull request #996 from nextstrain/dependabot/npm_and_yarn/packages_rs/nextclade-web/auspice-2.38.0 - [[`cc79e84`](https://github.com/nextstrain/nextclade/commit/cc79e844bafe9ea7d1748fca4c081fda8175ccf0)] chore: release web v2.5.1 - [[`bf21f97`](https://github.com/nextstrain/nextclade/commit/bf21f97d0265e8a82dddef9ad92a2ecfbc1c74fc)] Merge remote-tracking branch 'origin/master' into feat/escape - [[`44b1f9e`](https://github.com/nextstrain/nextclade/commit/44b1f9ecf6012f89c7663afd27058955f91ee732)] fix: correct escape algorithm - [[`125ac16`](https://github.com/nextstrain/nextclade/commit/125ac167a70ed6c3c0ca18d385d93e1ce6b17eac)] fix(web): ensure sorting results table by escape works - [[`ce1693a`](https://github.com/nextstrain/nextclade/commit/ce1693ac3759a29593ea190bbbb13f441b054408)] feat: add text to escape help tooltip - [[`3a502a9`](https://github.com/nextstrain/nextclade/commit/3a502a99cbe745d983535c74c59489b785283239)] Add clarification on when escape scores are unreliable - [[`b00e6c3`](https://github.com/nextstrain/nextclade/commit/b00e6c343019b195cd0f5e08d06f7166f5681ff5)] feat(web): make escape column tooltip wider - [[`9450041`](https://github.com/nextstrain/nextclade/commit/94500410f4a8c4f5fff981326d5265d5c1a57ecd)] feat: allow optional name different from gene name for escape values - [[`ac1b14a`](https://github.com/nextstrain/nextclade/commit/ac1b14a315c878c8c6b2ca4b3d3e22dcf99c05f7)] feat(web): add tooltips for escape column - [[`3cd1596`](https://github.com/nextstrain/nextclade/commit/3cd15961e39b735c965b92df7233071bf8eab7c1)] feat: skip escape calculation for outgroup samples - [[`e499dc7`](https://github.com/nextstrain/nextclade/commit/e499dc7cf7639144796f1e9aeaf37a17b59c72ac)] fix(web): sorting by escape - [[`2320822`](https://github.com/nextstrain/nextclade/commit/2320822c71194a579b467aa123fce18f71338f53)] feat: list ignored clades in the virus json - [[`e06e142`](https://github.com/nextstrain/nextclade/commit/e06e14260c9d6eef30b7e03c03aac21f983fb903)] feat: allow for escape coefs per posiition only and per posiition per aa - [[`dfbf64b`](https://github.com/nextstrain/nextclade/commit/dfbf64b9577fab162bfe13ca1a90b2d53c021aa4)] refactor: rename identifiers to clarify intent - [[`61e4fd7`](https://github.com/nextstrain/nextclade/commit/61e4fd7e7067146691ae7a4bea47878637b05aab)] refactor: lint - [[`6d28d49`](https://github.com/nextstrain/nextclade/commit/6d28d49a6084fc64f85dda2af393dc6aad26dfc6)] feat: render phenotype values in separate columns - [[`006396d`](https://github.com/nextstrain/nextclade/commit/006396d1639e5ce37a640fccc41099407837a436)] feat: use 'default' value if aa is not found in phenotype data - [[`0e20f4a`](https://github.com/nextstrain/nextclade/commit/0e20f4af63be4e0cc9e40cbd83fc5141c07e0310)] fix(web): fix custom column sorting - [[`f27d1b4`](https://github.com/nextstrain/nextclade/commit/f27d1b4b2115bd421d9218ff2910493b58b77b13)] feat(web): truncate phenotype values to 2 digits - [[`bf85198`](https://github.com/nextstrain/nextclade/commit/bf85198f1fb9e3424d949cae4772c2ea901656da)] feat(web): center phenotype value - [[`640e065`](https://github.com/nextstrain/nextclade/commit/640e065a28cd3c141e8bcd82bac04b971668d62f)] fix: avoid calling a method on undefined - [[`c82f35d`](https://github.com/nextstrain/nextclade/commit/c82f35d87976be612f86d034458c00dd5123e4fa)] feat(web): make phenotype columns different width from clades, narrower - [[`8718dad`](https://github.com/nextstrain/nextclade/commit/8718dadfd67b4e111c85fb9a46a1da8dbd91da88)] fix(web): read dataset name from URL, even when fasta is not provided Resolves: https://github.com/nextstrain/nextclade/issues/998 - [[`45c47c2`](https://github.com/nextstrain/nextclade/commit/45c47c200d4ce163065b344fc0be78046199c64c)] feat(web): show an indicator when dataset files are customized - [[`edcdc25`](https://github.com/nextstrain/nextclade/commit/edcdc25811d5639b760c066e8f5e43254b3c6fa4)] feat: replace some calls to unwrap() with proper error handling - [[`1b238b2`](https://github.com/nextstrain/nextclade/commit/1b238b2a8c49348cca08133a71eb45ad0250c962)] feat: improve error message - [[`b10aa40`](https://github.com/nextstrain/nextclade/commit/b10aa40f498c7157439d3d53eaf1cc4f0d498bee)] refactor: make function get_comp_level() infallible This function can never fail. Here I remove a call to unwrap(), which can never occur, by replacing traits, and remove error return type - [[`9de0bd2`](https://github.com/nextstrain/nextclade/commit/9de0bd24a6e255704dd1185641245a7e3d562362)] feat: replace some more calls to unwrap() with proper error handling Here I also introduce helper functions which return Result, to avoid long error handling boilerplate. - [[`477a837`](https://github.com/nextstrain/nextclade/commit/477a8376ad0b7da6d033116c9d170fc2a7e02143)] chore: upgrade rust to 1.63.0 - [[`5593f5e`](https://github.com/nextstrain/nextclade/commit/5593f5eee31f7a012746967bd23d44c361257669)] Merge remote-tracking branch 'origin/master' into feat/better-error-handling - [[`a975604`](https://github.com/nextstrain/nextclade/commit/a9756048228aebaa1b579ba751cbd76318f3b5d3)] refactor: use std::thread::scope instead of crossbeam::thread::scope As a better and mostly compatible alternative https://blog.rust-lang.org/2022/08/11/Rust-1.63.0.html#whats-in-1630-stable - [[`7e99cb9`](https://github.com/nextstrain/nextclade/commit/7e99cb9a49a0ca5007212a26627f67ec36ee7d93)] Merge pull request #999 from nextstrain/feat/web-url-read-dataset-without-fasta fix(web): read dataset name from URL, even when fasta is not provided - [[`8546969`](https://github.com/nextstrain/nextclade/commit/85469690eacac9db896555b0e3414f486bee5760)] Merge pull request #1000 from nextstrain/feat/better-error-handling - [[`4d24120`](https://github.com/nextstrain/nextclade/commit/4d241203df17b6e2553a9ee6c253fa48d9a32b2c)] Merge pull request #1001 from nextstrain/refactor/cli-std-thread-scope - [[`d618249`](https://github.com/nextstrain/nextclade/commit/d61824967c2c27e9131e3332c0651fb2b71477a4)] Merge remote-tracking branch 'origin/master' into feat/escape - [[`0713174`](https://github.com/nextstrain/nextclade/commit/0713174b48058c1691b6a7e9e1726b975645c790)] fix(web): fix phenotype attr marshaling when downloading csv/tsv Phenotype attrs were parsed into incorrect type when passed from JS to Rust - [[`9473ce8`](https://github.com/nextstrain/nextclade/commit/9473ce88d3b149d1c192edeeafea65666a36f982)] Merge pull request #990 from nextstrain/feat/escape - [[`9e0791a`](https://github.com/nextstrain/nextclade/commit/9e0791a782e725b61836ef520da718940ff88517)] chore: release web and cli 2.6.0 - [[`7fc59a1`](https://github.com/nextstrain/nextclade/commit/7fc59a1370a33b8d01a444679ed54037cf304009)] chore(ci): fix resource class 'small' not available CircleCI is failing with: "Resource class machine for small, image ubuntu-2004:202201-02 is not available for your project, or is not a valid resource class. " Let's try 'medium' class

Scientific Software - Peer-reviewed - Rust
Published by nextstrain-bot over 3 years ago

Nextclade - 2.5.0

Nextclade CLI 2.5.0, Nextclade Web 2.5.0 (2022-08-31)

Feature (CLI, Web): Coverage analysis

Nextclade now emits "coverage" metric which shows the portion of nucleotides in the alignment range being non-N and non-ambiguous, compared to the length of the reference sequence:

coverage = ((alignment_end - alignment_start) - total_missing - total_non_acgtns) / ref_len;

The metric is displayed as a percentage in the "Cov." column of Nextclade Web, and emitted into JSON, NDJSON, CSV and TSV outputs of Nextclade CLI and Web in the "coverage" field or column.

Feature (Web): Display machine-readable dataset names

Dataset selector on the main page of Nextclade Web now additionally shows machine-readable dataset name. This can help advanced Web users to put correct dataset name into the URL parameters, and CLI users to find the correct dataset name for downloads.

Feat (Web): Compact results table

We made some of the columns in results table of Nextclade Web narrower to make user experience a little better on laptops. When possible, for optimal experience, we still recommend to use 1080p displays or larger.

Fix (Web): Crashes when using filtering panel

Users reported intermittent crashes of Nextclade Web when entering values in the filtering panel on results page of Nextclade Web. This have been fixed now. If you stil have problems, please submit an issue in our GitHub repository.

Commit history

(click to expand)

- [[`b9a9a4b`](https://github.com/nextstrain/nextclade/commit/b9a9a4b5ece33e62768c82f94c7ce5b7666a71cd)] feat(web): show dataset machine-readable name in dataset selector - [[`2de9310`](https://github.com/nextstrain/nextclade/commit/2de9310c24a9cd3df9f4e5ecfd37bec0f3293210)] Merge remote-tracking branch 'origin/master' into feat/web-dataset-machine-readable-name - [[`4bad667`](https://github.com/nextstrain/nextclade/commit/4bad667dcf1606bacc995fa6402dceb0cbdeff7e)] fix: correctly reset duplicate sequence name map on new runs Currently duplicate sequence name data persists across unrelated runs of Nextclade Web, this causes incorrect reporting of duplicates. This PR ensures that duplicate sequence name data does not persist across runs. - [[`4f23954`](https://github.com/nextstrain/nextclade/commit/4f23954169bb78e8f02902165641974787a8c69e)] Merge pull request #950 from nextstrain/fix/web-dup-names-reset - [[`d4430e9`](https://github.com/nextstrain/nextclade/commit/d4430e9b0bdbfe85c9e09e807b50b5ab203392cc)] docs: add changelog for web 2.4.0 - [[`4435faf`](https://github.com/nextstrain/nextclade/commit/4435faf1751128fc5dde05d7dd45691f4ee20da8)] chore: release web v2.4.1 - [[`1cd8df0`](https://github.com/nextstrain/nextclade/commit/1cd8df057db291c3ffb341e0466200611c29bb21)] feat: calculate coverage qc metric - [[`4c2e5ed`](https://github.com/nextstrain/nextclade/commit/4c2e5ed153a6414e0c5b4c80e03db4492523a325)] feat: add coverage qc metric to csv and tsv outputs - [[`03cd444`](https://github.com/nextstrain/nextclade/commit/03cd444f28235a7a7e5e48aba7640d5c06d6f7a2)] feat(web): add coverage metric to web UI - [[`e8b59f1`](https://github.com/nextstrain/nextclade/commit/e8b59f1ac870f525f1e7e4af3aba6939be6074b5)] feat(web): correct and restyle download links on main page The currently deployed version links to non-existent v1 files. I thought that removing extra explanations (found in the docs) and making buttons more prominent will make it easier for users to discover these links. - [[`fab66aa`](https://github.com/nextstrain/nextclade/commit/fab66aa8572c3f0fa45ba21f6d2510ba56178343)] feat: add text suggested by @emmahodcroft - [[`c16836e`](https://github.com/nextstrain/nextclade/commit/c16836ed2d8f2141d5ef12b533836568e3260928)] doc: update about text in web app - [[`6aef071`](https://github.com/nextstrain/nextclade/commit/6aef071bcd2baef0004b24bedd34acab5028eaa2)] feat: add text suggested by @rneher - [[`418de94`](https://github.com/nextstrain/nextclade/commit/418de944a1a295b889d81b2e06e75d713945bede)] Merge pull request #960 from nextstrain/docs/update-about - [[`81b06c6`](https://github.com/nextstrain/nextclade/commit/81b06c6accaab823bdd05f71e6c64b7d46e6ce5f)] Merge pull request #958 from nextstrain/feat/download-links - [[`7309d2c`](https://github.com/nextstrain/nextclade/commit/7309d2ce396df9025f8286b68e7831a8a32e18d0)] Make coverage qc more sensitive - [[`a11499c`](https://github.com/nextstrain/nextclade/commit/a11499ca86cb25dd2573535eeab78591122e758f)] fix: wrong comment character - [[`caf3c9a`](https://github.com/nextstrain/nextclade/commit/caf3c9ae5d133908180fdbe21c80ee15a70166eb)] feat: remove indels from coverage calculation I'm not sure how handle Ns and ambiguous characters that appear in indels The formula as is assumes `missing` and `non_acgtns` don't count bases in indels - [[`92b0c26`](https://github.com/nextstrain/nextclade/commit/92b0c26eeca25cdaa68a9a6501c91e5932031d5d)] feat: remove coverage qc metric, move it into analysis results - [[`2412f63`](https://github.com/nextstrain/nextclade/commit/2412f634d374584d020a5c162c9ab273d7fb1797)] feat: remove qc metric from web app, add dedicated column - [[`ff9767b`](https://github.com/nextstrain/nextclade/commit/ff9767b42f31bab460e686f746e15c9679603b5c)] feat: add coverage column - [[`44e90db`](https://github.com/nextstrain/nextclade/commit/44e90db56b01ae68448fefcc373fb88c3118c7e8)] feat: add ref length and total covered nucs into file outputs - [[`b503c1b`](https://github.com/nextstrain/nextclade/commit/b503c1b4ec337e4580f06b1c61fc7bceb9abd264)] docs: fix links to nextalign downloads - [[`6b71d9e`](https://github.com/nextstrain/nextclade/commit/6b71d9ed6013acdd5c6cb8282463ce74e30239de)] docs: fix md syntax of a header - [[`18aa4e3`](https://github.com/nextstrain/nextclade/commit/18aa4e308c4dc566b71c85097f4ee0cada28f8b2)] Merge pull request #964 from nextstrain/docs/fixes - [[`a834ce1`](https://github.com/nextstrain/nextclade/commit/a834ce1ff16944251d3795265d122930afa8820f)] chore: add 'sphinx linkcheck' makefile target - [[`139c4a6`](https://github.com/nextstrain/nextclade/commit/139c4a61a84be53ba7a0aec6c7cfc2512d484157)] fix: doc links - [[`fd63ac8`](https://github.com/nextstrain/nextclade/commit/fd63ac8d8f84b305d37c6408a5d7fbc74a9749d5)] Merge pull request #965 from nextstrain/fix_doc_links - [[`984efc8`](https://github.com/nextstrain/nextclade/commit/984efc8c37f7015cfbab59bdcc21a444a9850aaa)] feat: add event analytics - [[`98c9076`](https://github.com/nextstrain/nextclade/commit/98c907622ca19e23d006c35e1ca71b982fc65c85)] Merge pull request #967 from nextstrain/feat/events - [[`c51184e`](https://github.com/nextstrain/nextclade/commit/c51184edb5bebd3b169936b63fdd9a07152deb2a)] chore: release web v2.4.2 - [[`739e5ed`](https://github.com/nextstrain/nextclade/commit/739e5ed8226afe6ad7d44b9bdf58cbb459c2d574)] Move coverage column after Ns - [[`e11a073`](https://github.com/nextstrain/nextclade/commit/e11a073f99af83b81ab7b22f0305a45f29017cbe)] Squeezing columns a bit - [[`1735cfd`](https://github.com/nextstrain/nextclade/commit/1735cfd89f587692aff7d13208df291738950d57)] chore: precompress web root AWS Cloudfront does not compress all files and we'd like to compress everything, including files larger than 10M and wasm for example. Here I compress files in advance with gzip and brotli and add a Lambda@Edge function which rewrites origin paths, depending on `accept-encoding` header. - [[`f6d167f`](https://github.com/nextstrain/nextclade/commit/f6d167f5f5fcf2feda3ae7752c1ef999428a649e)] chore: fix path - [[`a61c72f`](https://github.com/nextstrain/nextclade/commit/a61c72fbba9627cd9860e3112369ac2750a02bd1)] chore(ci): add missing deps - [[`5992d33`](https://github.com/nextstrain/nextclade/commit/5992d33e8b9872947f04d566fbdf507182255340)] chore(ci): ensure previously uploaded files are not erased - [[`c8356ab`](https://github.com/nextstrain/nextclade/commit/c8356ab8a2e405b756c4c003de6c7b45bd27a1b9)] chore: update security headers - [[`5c8c8cf`](https://github.com/nextstrain/nextclade/commit/5c8c8cf56d0dbc433c900b07025ea0b81c3e5109)] chore: fix typescript error - [[`16c741f`](https://github.com/nextstrain/nextclade/commit/16c741f583313f605974fe52361b8fdaff4a2068)] chore: install missing dependency - [[`5530c69`](https://github.com/nextstrain/nextclade/commit/5530c69339303fd2903e9be22b9534b3eab14050)] chore: update awscli - [[`ae0e6e5`](https://github.com/nextstrain/nextclade/commit/ae0e6e5af9324c0874eb3c35da36367a071a0ee9)] chore; set correct content type and encoding when deploying - [[`c3f5591`](https://github.com/nextstrain/nextclade/commit/c3f5591c03986da143515e8a735e7f0aa2aafbcc)] fix: make filtering code safer Related to: https://github.com/nextstrain/nextclade/issues/961 This removes casts in amino acid and nucleotide filtering code which have a potential to cause crashes in certain cases. I made `undefined`-comparison more lax, such that now it also checks for `null` and added default values to anything that can be nil. Even though I cannot reproduce the issue, this hopefully should fix it. - [[`d173af2`](https://github.com/nextstrain/nextclade/commit/d173af218851fa8cac28f1c16ea0d846ee7b0df3)] fix: swap array and filters Lodash `intersectionWith()` expects filtered array to be the first argument - [[`349a9e7`](https://github.com/nextstrain/nextclade/commit/349a9e7bc6c28b2bacd804ea12453c95fdddca4b)] chore(infra): fix .gz and .br rewrites - [[`b7e1e28`](https://github.com/nextstrain/nextclade/commit/b7e1e286d483425df737b16eaea3f3073521ee8a)] chore(infra): redirect from results and tree pages to main page [skip ci] They are not real pages, and there is nothing to see on these pages without running analysis first. - [[`f9d80b3`](https://github.com/nextstrain/nextclade/commit/f9d80b360fe67f25d597068157d1a1e8156db2b5)] feat: move coverage column - [[`d3cebfb`](https://github.com/nextstrain/nextclade/commit/d3cebfb275bda6b1980b1fb040eb440d5e9132b0)] Revert "feat: add ref length and total covered nucs into file outputs" This reverts commit 44e90db56b01ae68448fefcc373fb88c3118c7e8. - [[`8259f7e`](https://github.com/nextstrain/nextclade/commit/8259f7eb47b35c402bb63f3aee2e9fc1287e7e7b)] Merge pull request #962 from nextstrain/fix/filter-undefined-crash - [[`c01e8f0`](https://github.com/nextstrain/nextclade/commit/c01e8f0a84a000ceaf05871a275638992beb255d)] Merge pull request #956 from nextstrain/feat/coverage - [[`4c918a1`](https://github.com/nextstrain/nextclade/commit/4c918a11d130130a4e105759415a93dd0fe4d387)] Merge pull request #869 from nextstrain/feat/web-dataset-machine-readable-name - [[`a9da922`](https://github.com/nextstrain/nextclade/commit/a9da922489077685a95f12e9d6375d539e86b2f6)] chore: squeeze web table columns a bit more - [[`41d7c33`](https://github.com/nextstrain/nextclade/commit/41d7c33080542a973f0cd09f7aa6bfcabe84b7cc)] chore: prevent sorting arrows from disappearing - [[`8e48ce8`](https://github.com/nextstrain/nextclade/commit/8e48ce8c46042ca4bc78ae130982a77f09a00069)] Merge pull request #977 from nextstrain/squeeze-columns - [[`6a1b391`](https://github.com/nextstrain/nextclade/commit/6a1b391cc145f410c7aac81f1d59baaeac0b2d5e)] chore: release cli and web v2.5.0

Scientific Software - Peer-reviewed - Rust
Published by nextstrain-bot over 3 years ago

Nextclade - 2.4.0

Nextclade CLI 2.4.0, Nextclade Web 2.4.0 (2022-08-02)

Fix (Web): use indices to identify sequences uniquely in Nextclade Web

Previously, Nextclade used sequence names to identify sequences. However, sequence names proven to be unreliable - they are often duplicated. This caused various problems where results with the same names could have been overwritten.

Since this version, Nextclade Web is using sequence indices (order of sequences in the input file or files), to tell the sequences apart, uniquely. This should ensure correct handling of duplicate names. This change only affects results table in the Web application. CLI is not affected.

Feature (Web): warn about duplicate sequence names

Nextclade Web now reports duplicate sequence names. Duplicate sequence names often confuse bioinformatics tools, databases and bioinformaticians themselves, so we are trying to encourage the community to be more thoughtful about naming of their samples.

When duplicate names are detected during analysis in Nextclade Web, the "Sequence name" column of the results table now displays a yellow "duplicates" warning icon, and its tooltip contains a list of indices of sequences (serial numbers of the sequences in the input fasta file or files) having the same name.

Note that Nextclade compares only names, not sequence data themselves.

Feature (CLI): add "download dataset and run" shortcut"

In this version we added --dataset-name (-d) argument to run command, which allows to download a dataset with default parameters and run with it immediately, all in one command.

For example this command.

bash nextclade run --output-all=out --dataset-name=sars-cov-2 sequences.fasta or, the same, but shorter

bash nextclade run -O out -d sars-cov-2 sequences.fasta

will download the latest default SARS-CoV-2 dataset into memory and will run analysis with these dataset files. This is a convenience shortcut for the usual combination of nextclade dataset get + nextclade run. The dataset is not persisted on disk and downloaded on every run.

Feature (Web): Upgrade Auspice from version 2.37.2 to 2.37.3

This release includes a routine upgrade of Auspice tree view. You can read the changelog in the Auspice GitHub repository

Commit history

(click to expand)

- [[`5da4fe5`](https://github.com/nextstrain/nextclade/commit/5da4fe540e55a8de3d4ed7cab2bdc2a7b8203423)] chore(deps): bump auspice in /packages_rs/nextclade-web Bumps [auspice](https://github.com/nextstrain/auspice) from 2.37.2 to 2.37.3. - [Release notes](https://github.com/nextstrain/auspice/releases) - [Changelog](https://github.com/nextstrain/auspice/blob/master/CHANGELOG.md) - [Commits](https://github.com/nextstrain/auspice/compare/v2.37.2...v2.37.3) --- updated-dependencies: - dependency-name: auspice dependency-type: direct:production update-type: version-update:semver-patch ... Signed-off-by: dependabot[bot] - [[`5a9c699`](https://github.com/nextstrain/nextclade/commit/5a9c699ee0dfe3ea68ba74290c25c24efae53de2)] feat: assert mutation is inside the gene - [[`22e4e2d`](https://github.com/nextstrain/nextclade/commit/22e4e2d9d591c8d5969f3c0921422f216fe04ab7)] feat: add "download dataset and run" shortcut" This adds `--dataset-name` (`-d`) to `run` command, which allows to download a dataset with default parameters and run with it immediately, in one command. For example this command. ```bash nextclade run --output-all=out --dataset-name=sars-cov-2 sequences.fasta ``` will download the latest default sars-cov-2 into memory and will run analysis with these dataset files. This is a convenience shortcut for the usual combination of `dataset get` + `run`. The dataset is not persisted on disk and downloaded on every run. - [[`e155b94`](https://github.com/nextstrain/nextclade/commit/e155b94f66b1f200116f5714d72e9d06cd0cdc6d)] fix: use indices to identify sequences uniquely Nextclade is using sequence names to uniquely identify sequences. However, sequence names come from user inputs and cannot be trusted to be unique. Neither it seems there is a consensus on uniqueness of sequence names in the bioinformatics community as a whole. This causes various problems where sequence names are used as identifiers, and when for example there are multiple sequences with the same name. In particular, when storing analysis results, they are effectively stores in an associative container, where sequence name acts as a key. This leads to newer results overwriting older results as they arrive during analysis. Additionally, some of the HTML `id` properties used sequence names to add uniqueness. This was leading to incorrect HTML being produces, with multiple elements having the same `id` property. In this PR I: - change internal storage to use sequence indices in the input file(s) as keys - add sequence index into HTML `id`s - display "Sequence index" in places where only sequence name was displayed previously This should ensure correct handling of duplicated names. This affects only web application. In the algorithmic and CLI parts, sequence names are not used - results are stored in the form of an array, and no HTML is involved. - [[`c43367e`](https://github.com/nextstrain/nextclade/commit/c43367ec1b5fd4eb3944a851a07bba0a1f8143dc)] Merge remote-tracking branch 'origin/master' into fix/web-unique-seq-ids - [[`e744ca6`](https://github.com/nextstrain/nextclade/commit/e744ca673856d6dba2db2068db62bb348d32a227)] chore: release web v2.3.1 - [[`e2f37d7`](https://github.com/nextstrain/nextclade/commit/e2f37d7a928172a335646ccbe971f7ca695b3a0d)] chore: fix CHANGELOG link to PR instead of issue - [[`2a88f30`](https://github.com/nextstrain/nextclade/commit/2a88f30f914989cf901bb12dd4890923ad722dfe)] Merge pull request #938 from nextstrain/fix/crash-gene-overflow - [[`c92683a`](https://github.com/nextstrain/nextclade/commit/c92683ab8e2698db17325eb61c847ce83905716e)] Merge pull request #939 from nextstrain/feat/dataset-get-and-run - [[`8a69ac7`](https://github.com/nextstrain/nextclade/commit/8a69ac764417465ca91c35e79d76276a980af7c0)] feat: remove sequence index from tooltips - [[`ec2104a`](https://github.com/nextstrain/nextclade/commit/ec2104a2bb6ffe62871fee98c678e139332d3147)] Merge pull request #946 from nextstrain/fix/web-unique-seq-ids - [[`92a7234`](https://github.com/nextstrain/nextclade/commit/92a723446ec7117a99176d9a02608974a796277d)] feat(web): report duplicate sequence names This adds little yellow icons in the "Sequence name" column when a sequence has the same name as other sequences in the same run. Indices of these sequences are additionally listed in the tooltip. - [[`a02b60c`](https://github.com/nextstrain/nextclade/commit/a02b60c89c7a40a90702293f911eac6e83c88a55)] docs: add changelog for 2.4.0 - [[`a2c37ad`](https://github.com/nextstrain/nextclade/commit/a2c37ad637a82ed36bdcd9498cfef114850fa70e)] Merge pull request #937 from nextstrain/dependabot/npm_and_yarn/packages_rs/nextclade-web/auspice-2.37.3 chore(deps): bump auspice from 2.37.2 to 2.37.3 in /packages_rs/nextclade-web - [[`5cb0f15`](https://github.com/nextstrain/nextclade/commit/5cb0f153cfd5077d01d955627d627eaf30771ca3)] Merge pull request #948 from nextstrain/feat/web-report-dup-seq-names feat(web): report duplicate sequence names - [[`d11f14f`](https://github.com/nextstrain/nextclade/commit/d11f14fd4985756bd01b0b8712cac538fcf20b18)] docs: extend changelog for 2.4.0 - [[`1f9b80d`](https://github.com/nextstrain/nextclade/commit/1f9b80d530f6151fee366ca97db06ebd7e06c145)] chore: release cli 2.4.0 and web v2.4.0

Scientific Software - Peer-reviewed - Rust
Published by nextstrain-bot over 3 years ago

Nextclade - 2.3.1

Nextclade CLI 2.3.1, Nextclade Web 2.3.1

Fix #947: In datasets where genes started right at the beginning of the reference sequence, Nextclade version 2.0.0 until 2.3.0 will crash due to underflow. This is now fixed. The only Nextclade provided dataset that was affected by this bug is Influenza Yamagate HA. That dataset had a further bug in the tree so there is now a corresponding dataset bug fix release available. (report: @mcroxen)

Commit history

(click to expand)

- [[`36e2d8f`](https://github.com/nextstrain/nextclade/commit/36e2d8fe7e553fdadc7c6b5df686d9769471ce4d)] chore: release web v2.3.0 - [[`329b5e3`](https://github.com/nextstrain/nextclade/commit/329b5e3c696cbf2f9e8f04ad0bb2ccc42607300c)] Check for auspice updates daily Uses dependabot to check for auspice updates. - [[`f07a807`](https://github.com/nextstrain/nextclade/commit/f07a80743b15f6f44b385ea206e1520fc2d963e7)] Delete Update-Auspice.yml This is not needed with the new .github/dependabot.yml. - [[`1395627`](https://github.com/nextstrain/nextclade/commit/13956274ab305bf42f5ecee84969cc78df49cb91)] Merge pull request #936 from victorlin/master - [[`f4c1aa3`](https://github.com/nextstrain/nextclade/commit/f4c1aa38bb448dd5d09f176bc60106300462cbb3)] docs: adjust cli docs to nextclade v2 - [[`781e998`](https://github.com/nextstrain/nextclade/commit/781e9984aef0e4aa390f13e757281b8e79256b6a)] Merge pull request #941 from nextstrain/docs/v2 - [[`572915b`](https://github.com/nextstrain/nextclade/commit/572915bab56f215e805544a9f95bcc1e8c4e50f4)] docs: Install nextstrain.sphinx.theme extension The new extension has sphinx_copybutton pre-installed and configured. This change enables it here. This also makes it easier to configure other extensions across multiple docs projects. - [[`23010b7`](https://github.com/nextstrain/nextclade/commit/23010b7b5dc675534cf1a492111e6f3cedc29ad3)] Bump nextstrain-sphinx-theme to >=2022.5 This is when the extension started being actively configured. - [[`4fd46af`](https://github.com/nextstrain/nextclade/commit/4fd46af22d7cf9f5fcb16ea03245c9d79dc896a3)] Merge pull request #943 from nextstrain/victorlin/docs-install-nextstrain-extension docs: Install nextstrain.sphinx.theme extension - [[`11f6fcb`](https://github.com/nextstrain/nextclade/commit/11f6fcbcdb06cd8788629150b194d4433872b5fd)] chore: add tmp data to gitignore - [[`2d8ab9d`](https://github.com/nextstrain/nextclade/commit/2d8ab9d5384f2a7eec97f3f083a41543c1e94383)] refactor: lint - [[`2f9d677`](https://github.com/nextstrain/nextclade/commit/2f9d67795eb107ed637ad6c675f7b845c61d951e)] Merge pull request #945 from nextstrain/lint - [[`316862e`](https://github.com/nextstrain/nextclade/commit/316862e888a7891e51a943544eb609fcec5f5d2f)] fix: underflow when mutation in gene close to start When the first gene is very close to the start of the sequence - [[`921a11b`](https://github.com/nextstrain/nextclade/commit/921a11bd61761b2ac9270d07993fb633993a9d88)] Merge pull request #947 from nextstrain/fix/underflow-gene-context fix: underflow when mutation in gene close to start - [[`5cc22de`](https://github.com/nextstrain/nextclade/commit/5cc22deb9da32fbe6332d58af113aee1dc7a7976)] chore: CHANGELOG for 2.3.1 - [[`e737f19`](https://github.com/nextstrain/nextclade/commit/e737f19c47b335e71bc1a5af47821bd62f5a68c7)] chore: release cli 2.3.1

Scientific Software - Peer-reviewed - Rust
Published by nextstrain-bot over 3 years ago

Nextclade - 2.3.0

Nextclade CLI 2.3.0, Nextclade Web 2.3.0

This release brings back entries for failed sequences into output files.

It was reported by @tseemann (https://github.com/nextstrain/nextclade/issues/921) that in Nextclade v2 CSV and TSV rows are not written for failed sequences. While in v1 they were. This was unintended.

In this release:

CSV, TSV, NDJSON rows for failed entries are now also written (only seqName and errors columns are populated). Note, it's important to check for errors column and disregard other columns if there are errors. For example, in case of an error, the substitutions column will be empty, but it does not mean that the failed sequence has no substitutions.
JSON output now has a separate errors field at the root of the object, with all failed entries
NDJSON rows are also written for failed entries. They only contain index, seqName and errors fields.
new columns are written into CSV and TSV outputs: warnings and failedGenes, which include any warnings emitted for a sequence as well as a list of genes that failed translation. Now all columns of the "errors.csv" file are also in the CSV and TSV results files

We improved the warning that users of unsupported browsers (mostly Safari) receive when they browse to Nextclade web.

Rust

Nextclade core algorithms and command-line interface was reimplemented in Rust (replacing C++ implementation).

Rust is a modern, high performance programming language that is pleasant to read and write. Rust programs have comparable runtime performance with C++, while easier to write. It should provide a serious productivity boost for the dev team.

Also, it is now much simpler to contribute to Nextclade. If you wanted to contribute, or to simply review and understand the codebase, but were scared off by the complexity of C++, then give it another try - the Rust version is much more enjoyable! Check our developer guide for getting started. We are always open for contributions, reviews and ideas!

Alignment algorithm rewritten with adaptive bands

Feature: Previously, the alignment band width was constant throughout a given sequence. Now, band width is adaptive: narrow where seed matches indicate no indels, wide where seed matches indicate indels.
Performance is improved for sequences with indels
Fix: Terminal alignment errors, particularly common in BA.2, are fixed due to wider default band width between terminal seed matches and sequence ends
Fix: More robust seed matching allows some previously unalignable sequences to be aligned
Fix: Terminal indels for amino acid alignments are only free if the nucleotide alignment indicates a gap. Otherwise, they are penalized like internal gaps. This leads to more parsimonious alignment results.
Feature: Additional alignment parameters can now be tuned:
- "Excess band width" parameter controls the extra band width that is necessary for correct alignment if both deletions and insertions occur between two seed matches.
- "Terminal band width" controls the extra band width that is necessary for correct alignment if terminal indels occur.
Feature: "Min match rate" parameter is added, which sets required rage of seed matches in a sequence (number of matched seeds divided by total number of attempted seeds). If the measured rate is below required, alignment will not be attempted, as for such sequences, there is a high chance of infeasible memory and computational requirements. The default value is 0.3.
Fix: 3' terminal insertions are now properly detected
Feature: "Retry reverse complement" alignment parameter is added. When enabled, an additional attempt of seed matching is made after initial attempt fails. The second attempt is performed on reverse-complemented sequence.

As a consequence: - the output alignment, peptides and analysis results correspond to this modified sequence and not to the original - sequence name gets a suffix appended to it for all output files (fasta, seqName column, node name on the tree etc.) - in output files, there is a new field/column: isReverseComplement, which contains true if the corresponding sequence underwent reverse-complement transformation

This functionality is opt-in and the default behavior is unchanged: skip sequence and emit a warning.

Genes on reverse (negative) strand

Nextclade now correctly handles genes on reverse (negative) strand, which is particularly important for Monkeypox virus.

Nextclade Web

Feature: Nextclade Web is now substantially faster, both to startup and when analysing sequences, due to general algorithmic improvements.
Feature: Drag&drop box for fasta files now supports multiple files. The files are concatenated in this case.
Feature: Sequence view and peptide views now show insertions. They are denoted as purple triangles.
Fix: Tree view now longer shows duplicate clade annotations

Input files

Fix: gene map GFF3 file now correctly accepts "gene" and "locus_tag" attributes. This should allow to use genome annotations from GeneBank with little or no modifications.
Feature: Nextclade now reads virus-specific alignment parameters from virus_properties.json file from the dataset. It is equivalent to passing alignment tweaks using command-line flags, but is more convenient. If a parameter is provided in both virus_properties.json and as a flag, then the flag takes precedence.

Nextclade CLI

Feature: BREAKING CHANGE Command-line interface was redesigned to make it more consistent and ergonomic. The following invocation should be sufficient for most users:

bash nextclade run --input-dataset=dataset/ --output-all=out/ sequences.fasta

short version:

bash nextclade run -D dataset/ -O out/ sequences.fasta

Nextalign CLI and Nextclade CLI now require a command as the first argument. To reproduce the behavior of Nextclade v1, use nextalign run instead of nextalign and nextclade run instead of nextclade. See nextalign --help or nextclade --help for the full list of commands. Each command has it own --help menu, e.g. nextclade run --help.
--input-fasta flag is removed in favor of providing input sequence file names as positional arguments. Multiple input fasta files can be provided. Different compression formats are allowed:

bash nextclade run -D dataset/ -O out/ 1.fasta 2.fasta.gz 3.fasta.xz 4.fasta.bz2 5.fasta.zst
If no fasta files provided, it will be read from standard input (stdin). Reading from stdin does not support compression.
If a special filename (-) is provided for one of the individual output file flags (--output-*), the corresponded output will be printed to standard output (stdout). This allows integration into Unix-style pipelines. For example:

```bash curl $fastagzurl | gzip -cd | nextclade run -D dataset/ --output-tsv=- | mynextcladetsv_processor

xzcat *.fasta.xz | nextalign run -r ref.fasta -m genemap.gff -o - | processalignedfasta ```
The flag --output-all (-O) replaces --output-dir flag and allows to conveniently output all files with a single flag.
The new flag --output-selection allows to restrict what's being output by the --output-all flag.
If the --output-basename flag is not provided, the base name of output files will default to "nextclade" or "nextalign" respectively for Nextclade CLI and Nextalign CLI. They will no longer attempt to guess base file name from the input fasta.
The new flag --output-translations is a dedicated flag to provide a file path template which will be used to output translated gene fasta files. This flag accepts a template string with a template variable {gene}, which will be substituted with a gene name. Each gene therefore receives it's own path. Additionally, the translations are now independent from output directory and can be omitted if they are not necessary.

Example:

If the following is provided:

```bash
--output-translations='output_dir/gene_{gene}.translation.fasta'
```

then for SARS-CoV-2 Nextclade will write the following files:

```
output_dir/gene_ORF1a.translation.fasta
output_dir/gene_ORF1b.translation.fasta
...
output_dir/gene_S.translation.fasta
```

Make sure you properly quote and/or escape the curly braces in the variable {gene}, so that your shell, programming language or pipeline manager does not attempt to substitute the variable.

Feature: New --excess-bandwidth, --terminal-bandwidth, --min-match-rate, --retry-reverse-complement arguments are added (see "Alignment algorithm rewritten with adaptive bands" section for details)
Feature: Nextclade CLI and Nextalign CLI now accept compressed input files. If a compressed fasta file is provided, it will be transparently decompressed. Supported compression formats: gz, bz2, xz, zstd. Decompressor is chosen based on file extension.
Feature: Nextclade CLI and Nextalign CLI can now write compressed output files. If output path contains one of the supported file extensions, it will be transparently compressed. Supported compression formats: gz, bz2, xz, zstd.
Feature: Nextclade can now write outputs in newline-delimited JSON format . Use --output-ndjson flag for that. NDJSON output is equivalent to JSON output, but is not hierarchical, so it can be easily streamed and parsed one entry at a time.
Feature: Nextclade dataset get and dataset list commands now can fetch dataset index from a custom server. The root URL of the dataset server can be set using --server=<URL> flag.
Feature: Nextclade dataset get command can output downloaded dataset in the form of a zip archive, using --output-zip flag. The dataset zip is simply the dataset directory, but compressed, and it can be used as a replacement in the --input-dataset flag of the run command.
Feature: Nextalign CLI and Nextclade CLI provide a command for generating shell completions: see nextclade completions --help for details.
Feature: Verbosity of can be tuned using wither --verbosity=<severity> flag or one or multiple occurences of -v and -q flags. By default Nextclade and Nextalign show messages with severity "warn" or above (i.e. only warning and errors). Flag -v increases and flag -q decreases verbosity one step, -vv and -qq - two steps, etc.

Feedback

If you found a bug or have a suggestion, feel free to:

submit a new issue on GitHub: nextstrain/nextclade
fork the Nextclade GitHub repository nextstrain/nextclade and contribute a bugfix or an improvement (see dev guide)
join Nextstrain discussion forum: discussion.nextstrain.org for a free-form discussion

| ⚠️ | This is a pre-release. It can contain bugs and significant changes which are not yet finalized. Changes may appear without notice. We recommend to try the pre-releases to learn about upcoming features. For important projects, use stable releases. | |:---:|:---|

See the changelog: https://github.com/nextstrain/nextclade/blob/master/CHANGELOG.md#nextclade-200

Commit history

(click to expand)

- [[`1ec1c2b`](https://github.com/nextstrain/nextclade/commit/1ec1c2b0726221b301e4d31e8443d792852f312c)] feat(web): add warning for unsupported browsers - [[`c91d006`](https://github.com/nextstrain/nextclade/commit/c91d0060933b0a636083b7639e8169c85b9a4501)] Merge pull request #866 from nextstrain/feat/web-unsipported-browser-warning - [[`0288991`](https://github.com/nextstrain/nextclade/commit/0288991bbd5ed18a2e6eb14026d86f229a4836dd)] chore: release web v2.1.0 - [[`9d056b1`](https://github.com/nextstrain/nextclade/commit/9d056b1787f1680493caa7a8c7714ae7dbc7eb9d)] chore(ci): ensure correct full domain var is set for web app builds - [[`c2d1459`](https://github.com/nextstrain/nextclade/commit/c2d1459ece55d3e25cf53f758ad030380fa00e54)] fix(web): ensure init errors are not hidden Nextclade Web has been hiding some of the errors that occur during initialization. Notably, if dataset server is not reachable or dataset index fetch fails for any reason, then Nextclade would just show loading spinner indefinitely. This PR ensures that the error is properly handled and that an error message is shown in these cases. - [[`36f0df7`](https://github.com/nextstrain/nextclade/commit/36f0df7832e9ad6cafacbd9213c7dfcd2532eeda)] Merge pull request #867 from nextstrain/fix/web-init-hidden-errors - [[`21c8568`](https://github.com/nextstrain/nextclade/commit/21c856860102588d2ebc82242e72c5a68b5d1325)] feat(cli): improve error message when old, removed cli args are used - [[`b4f0559`](https://github.com/nextstrain/nextclade/commit/b4f0559b92a89b3ebea482e5caa8955e7586674c)] Merge pull request #868 from nextstrain/feat/cli-better-errors-on-removed-args - [[`013eed6`](https://github.com/nextstrain/nextclade/commit/013eed6ee69c8418966a13a330404ca53e39f084)] chore: release cli 2.0.0-beta.2

Scientific Software - Peer-reviewed - Rust
Published by nextstrain-bot over 3 years ago

Nextclade - 2.0.0-beta.1

| ⚠️ | This is a pre-release. It can contain bugs and significant changes which are not yet finalized. Changes may appear without notice. We recommend to try the pre-releases to learn about upcoming features. For important projects, use stable releases. | |:---:|:---|

| ⚠️ | This is a pre-release. It can contain bugs and significant changes which are not yet finalized. Changes may appear without notice. We recommend to try the pre-releases to learn about upcoming features. For important projects, use stable releases. | |:---:|:---|

Nextclade Web 1.14.0, Nextclade CLI 1.11.0, Nextalign CLI 1.11.0 (2022-03-15)

[Feature] Nextclade Pango classifier (SARS-CoV-2 specific)

With the latest dataset, Nextclade now assigns sequences a pango lineage, similar to how clades are assigned. The classifier is about 98% accurate for sequences from the past 12 months. Older lineages are deprioritised, and accuracy is thus worse. Read more about the method and validation against pangoLEARN and UShER in this report: Nextclade as pango lineage classifier: Methods and Validation.

[Feature] Better tree extensions #741

The Nextclade extensions fields in reference tree JSON now contain more information. This makes custom clade-like columns on the results page more informative.

[Feature] Update Auspice

The tree rendering component, Auspice, was updated to version 2.34.1. Refer to its changelog for details.

[Fix] Mutation badges showing incorrect position for first nucleotide #745

We fixed a bug where mutations at position 1 were incorrectly showing position 0 in Nextclade Web

Scientific Software - Peer-reviewed - Rust
Published by ivan-aksamentov almost 4 years ago

Nextclade - 1.10.3

Nextclade Web 1.13.2, Nextclade CLI 1.10.3, Nextalign CLI 1.10.3 (2022-02-15)

This is a bug fix release.

[Fix] Ignore private reversions of deletions when calculating divergence

Since their introduction, individual private reversions of deletions contributed extra to divergence. This was unexpected, so we removed reversions of deletions from consideration when calculating divergence in Nextclade.

[Fix] Sort private substitutions on the tree

Private substitutions are now sorted by position when they are displayed on the tree page

[Fix] "truncated" text in the insertions tooltip

In Nextclade Web, long insertions no longer have a visual bug when the "truncated" text is displayed twice.

Scientific Software - Peer-reviewed - Rust
Published by ivan-aksamentov about 4 years ago

Nextclade - 1.10.2

Nextclade Web 1.13.1, Nextclade CLI 1.10.2, Nextalign CLI 1.10.2 (2022-02-01)

This is a bug fix release.

[Fix] Exclude reversions of deletions from consideration in "SNP clusters" QC rule

Since introduction of reversions in Nextclade Web 1.13.0 and Nextclade CLI 1.10.0, "SNP clusters" QC rule have been including reversions of deletions when counting clustered private mutations. This was unexpected and produced false-positives for some of the sequences. To fix that, we removed the reversions of deletions from consideration of this QC rule, so that it behaves as previously.

[Fix] Center markers in sequence view in Nextclade Web

In this version we improved the display of various colored markers (mutations, ranges etc.) in sequence and peptide views on the Results page of Nextclade Web. The individual markers are now centered around their position in the sequence (previously left-aligned). Although markers have moved by just a few pixels, this makes positioning more consistent, and ensures that different types of markers are correctly aligned across table rows.

Scientific Software - Peer-reviewed - Rust
Published by ivan-aksamentov about 4 years ago

Nextclade - 1.10.1

Nextclade CLI 1.10.1 (2022-01-26)

[Fix] Improve error message when the virus properties file is missing #704

Since version 1.10.0 Nextclade CLI have introduced a new required input file, virus_properties.json and datasets and documentation were updated to match. However, users who don't use datasets might have encountered breakage due to a missing file: when running Nextclade CLI without either --input-dataset of --input-virus-properties flag provided, it would stop with an unclear error message. In this release we improve the error message, making sure that that explains the problem and offers a solution.

This does not affect Nextclade Web or Nextalign CLI.

In order to facilitate upgrades, for most users, we recommend to:

download the latest dataset before each Nextclade CLI session (e.g. in the beginning of an automated workflow, or once you start a batch of experiments manually) using nextclade dataset get command
use --input-dataset flag instead of individual --input-* flags for dataset files when issuing nextclade run command
if necessary, override some of the individual input files using corresponding --input-* flags

[Fix] Add information about `virus_properties.json` or `--input-virus-properties` to changelog

In the excitement of bringing the new features, we forgot to mention virus_properties.json or --input-virus-properties in the changelog when Nextclade CLI 1.10.0 was released. We now added this information retroactively.

Scientific Software - Peer-reviewed - Rust
Published by ivan-aksamentov about 4 years ago

Nextclade - 1.10.0

Nextclade Web 1.13.0, Nextclade CLI 1.10.0, Nextalign CLI 1.10.0 (2022-01-24)

💥 [BREAKING CHANGE] Nextclade: new required input file: `virus_properties.json` #689

This version introduces a new required input file for Nextclade, called virus_properties.json. This file contains additional information necessary for the "Detailed split of private mutations" feature (see below). The new versions of Nextclade datasets were released to account for this change.

How it affects different tools in the Nextclade family and how to upgrade:

Nextclade Web - requires the new file. Migration path: no action is needed. Nextclade Web always uses the latest dataset automatically.
Nextclade CLI - requires the new file. Migration path:
- Download the latest dataset with nextclade dataset get command (dataset tagged 2022-01-18T12:00:00Z or more recent is required)
- If using --input-dataset flag: the new file will be be picked up automatically from the latest dataset. No further action is needed.
- If not using --input-dataset flag: add --input-virus-properties flag to point to virus_properties.json file from the dataset.
Nextalign CLI - not affected: it does not use virus_properties.json. Migration path: no action is needed.

[Feature] Detailed split of private mutations (Nextclade) #689

Private mutations (differences between a query sequence and nearest neighbour in reference tree) are now split into three categories:

Reversion to reference genotype
(SARS-CoV-2 only for now) Mutation to a genotype common in at least 1 clade get labeled with that clade
Mutations that are neither reversions nor labeled (called "unlabeled")

Which category a mutation belongs to is visible by hovering over the "Mut." column in Nextclade Web and in various "privateNucMutations" fields in csv/tsv/json outputs.

[Change] "Private mutations" QC rule now accounts for reversions and labeled mutations

Reversions and labeled mutations (see feature above) are particularly common in contaminated samples, coinfections and recombination. To draw the user's attention to such sequences, both types of private mutation now get higher weights in the "Private mutations" QC rule (denoted as "P" in Nextclade Web, and qc.privateMutations in output files).

[Feature] Insertions now also available as amino acids #692

Aminoacid insertions in the query peptides relative to the corresponding reference peptide are now displayed in the "Ins." column in Nextclade Web and are emitted as "aaInsertions" and "totalAminoacidInsertions" fields in Nextalign and Nextclade output files. Note, that similarly to nucleotide insertions, aminoacid insertions are stripped from the output alignment.

[Fix] Gaps in query sequences are now stripped correctly #696

When query sequences contained gaps (-), e.g. when inputting aligned sequences, gaps were not stripped correctly since v1.7.0 (web v1.10.0), which could lead to - showing up in insertions.

Scientific Software - Peer-reviewed - Rust
Published by ivan-aksamentov about 4 years ago

Nextclade - 1.9.0

Nextclade Web 1.12.0, Nextclade CLI 1.9.0, Nextalign CLI 1.9.0 (2022-01-11)

[Feature] Handle "-" strand gene translation

The strand column in the gene map file was previously ignored. Now the "-" strand genes are correctly reverse-complemented before translation. Thanks @dnanto for the contribution.

[Feature] Update SARS-CoV-2 clade schema

The schema that illustrates the tree of SARS-CoV-2 clades on the main page of Nextclade Web was updated to account for recent clade changes.

[Fix] Center mutation markers in sequence views

Previously the mutation markers in sequence views in results table of Nextclade Web were anchored to their position in the sequence view on their left edge. They are now correctly centered around their position, such that the center of marker is at the corresponding position in the sequence.

[Fix] Correct exit codes

Nextclade CLI and Nextalign CLI could sometime exit with incorrect exit code. This has been fixed.

[Fix] Correctly handle empty peptides

The alignment algorithm in Nextclade CLI and Nextalign CLI could sometimes produce translation that is longer than expected, when the translated sequence is empty. Now the empty peptides are discarded and a warning is issued.

[Fix] Ensure array boundaries

In rare cases Nextclade and Nextalign algorithms could sometimes read past the end of arrays, which previously went undetected. This is now fixed.

Scientific Software - Peer-reviewed - Rust
Published by ivan-aksamentov about 4 years ago

Nextclade - 1.8.1

Nextclade Web 1.11.1, Nextclade CLI 1.8.1 (2022-01-07)

[Hotfix] Nextclade CLI crashes on macOS when reading JSON tree (#680)

Fixes crash with Error: [json.exception.invalid_iterator.214] cannot get value | when reading JSON tree on macOS

Scientific Software - Peer-reviewed - Rust
Published by nextstrain-bot about 4 years ago

Nextclade - 1.8.0

Nextclade Web 1.11.0, Nextclade CLI 1.8.0 (2022-01-04)

[Feature] Better dataset selector

Nextclade Web has got the new dataset selector on the main page, which clearly presents all available datasets and is more convenient to use. The last selected dataset is remembered, so that it does not need to be selected again on subsequent runs. This also fixes rare problems and inconsistencies, when incorrect dataset might have been used despite another dataset is being selected.

[Feature] Dynamic node attributes

Nextclade CLI and Nextclade Web now can assign multiple clade-like attributes to the analyzed sequences.

If input reference tree JSON contains an array of attribute keys attached to the

meta.extensions.nextclade.clade_node_attrs_keys = ["my_clades", "other_clades"]

For each query sequence, during clade assignment step, Nextclade will lookup values of these keys from .node.node_attrs property of the nearest reference tree node and assign them to the corresponding properties of the newly attached nodes, just like it happens with the usual Nextstrain clades. This feature is currently not used with the default datasets, but we are planning to extend the reference trees in these datasets to take advantage of this feature. Curious users can start experimenting with their own reference trees and custom nomenclatures. Learn more about clade assignment in Nextclade in the documentation.

[Performance] Optimize match table lookups

In this version, alignment algorithm behind Nextclade and Nextalign is up to 10% faster due to performance improvements in nucleotide and aminoacid table lookups.

Scientific Software - Peer-reviewed - Rust
Published by nextstrain-bot about 4 years ago

Nextclade - 1.7.0

Nextclade Web 1.10.0, Nextclade CLI 1.7.0 (2021-12-09)

[Performance] Optimize FASTA parser

The new optimized FASTA parser makes Nextclade CLI up to 60% faster and Nextalign CLI up to 500% faster when used on high-core-count machines. Nextalign and Nextclade now scale much better with number of available threads and rely less on I/O speed. See #632 for more details.

[Fix] Avoid crash due to buffer overflow

This is an internal fix of a problem that might have lead to a crash in rare cases, when coordinate map array was accessed beyond it's size.

Scientific Software - Peer-reviewed - Rust
Published by nextstrain-bot about 4 years ago

Nextclade - 1.6.0

Nextclade Web 1.9.0, Nextclade CLI 1.6.0 (2021-12-07)

[BREAKING CHANGE] [Fix] Remove unused CLI flags for aminoacid seed alignment

Seed matching step was removed in Nextalign and Nextclade CLI 1.5.0, however the command-line parameters previously providing configuration options for this step were not. In this version, the now unused family of --aa-* CLI flags is removed. Migration path: remove these flags from Nextclade CLI invocation.

[Feature] Make "results" and "tree" pages full-width in Nextclade Web

The content in "results" and "tree" pages of Nextclade Web now occupies entire width available in the browser window, so that more useful information can be presented. In particular, sequence views should be more readable, especially on larger screens.

[Feature] Dynamically adjust width of AA mutation markers

Nextclade Web now dynamically adjusts width of AA mutation markers in sequence views to avoid overly long mutation groups that may obscure other mutations. This is particularly important for sequences with high density of mutations.

[Feature] Reduce probability of WebWorker timeout errors

On low-end computers, computers with slow internet connection or computers under heavy background resource utilization Nextclade Web could sometimes produce WebWorker timeout errors. This has been addressed by increasing the timeout interval from 10 seconds to 1 minute.

If this is not enough, consider freeing up system memory and CPU resources by closing unused applications and browser tabs, processing sequences in smaller batches, or using Nextclade CLI.

[Fix] Fix off-by-one errors in insertion positions

Nextclade Web, Nextclade CLI and Nextalign could sometime produce incorrect positions for nucleotide insertions - off by 1 nucleotide to either direction. This was fixed in the new version.

[Fix] Don't add private reversions when query aminoacid is unknown

In previous versions, if a query sequence, for one reason or another, had aminoacid X at the position where the parent tree node had a private mutation, Nextclade was incorrectly calling a new reversion at this position. This is now fixed and Nextclade will not report a reversion. We assume that in these situations the sequencing defect is more likely than a reversion.

[Fix] Avoid potential dereference of nullopt

This is an internal fix of a problem that might have lead to a crash, but never manifested so far.

[Fix] Avoid error when `--genes` flag contains a subset of genes

Nextclade 1.8.0 introduced an error when --genes flag contained only a subset of genes from the gene map. This is now resolved.

Scientific Software - Peer-reviewed - Rust
Published by ivan-aksamentov about 4 years ago

Nextclade - 1.5.1

Nextclade Web 1.8.1, Nextclade CLI 1.5.1 (2021-11-27)

[Fix] Avoid crash when relative shift (bandwidth) is larger than query length

In rare cases Nextclade 1.5.0 could crash during alignment of some of the short peptides. This has been fixed in this version.

[Fix] Improve peptide alignment

We improved heuristics which determine band width and shift for the peptide alignment, so that some of the peptides with large insertions can now be aligned.

Scientific Software - Peer-reviewed - Rust
Published by ivan-aksamentov over 4 years ago

Nextclade - 1.5.0

Nextclade Web 1.8.0, Nextclade CLI 1.5.0 (2021-11-27)

[Feature] Improve peptide alignment

We improved the algorithm for peptide alignment. Instead of performing seed matching in order to estimate width of the band and shift parameters for peptide alignment, we now deduce these parameters from the nucleotide alignment results. This allows Nextclade to align and analyse some of the peptides that would fail previously, including for low quality gene sequences and sequences with large deletions or deletions close to the beginning.

[Fix] Account for the partially covered last codon in frame shift

Nextclade previously did not account for the last codon in a frame shift if that codon was covered by the shift only partially. In this version we count the partial codons. This solves an issue with empty frame shift codon ranges being reported in rare cases. This change may result in some of the frame shifts to be longer by 1 codon in the new version compared to previous versions of Nextclade. The nucleotide length of frame shifts stays the same.

None of the ignored frame shift ranges in the QC configurations of the exising dataset are affected by this change. But if you use a custom QC configuration, some of the frame shifts in the list of ignored frame shifts might need to be be adjusted.

[Fix] Fix crashes with Nextclade CLI on macOS

In this version we fixed a crash with segmentation fault that could sometimes happen with Nextclade CLI on macOS.

Scientific Software - Peer-reviewed - Rust
Published by ivan-aksamentov over 4 years ago

Nextclade - 1.4.5

Nextclade Web 1.7.3, Nextclade CLI 1.4.5 (2021-11-04)

This is a bugfix release for Nextclade Web and Nextclade CLI.

After Nextclade Web version 1.7.3 and Nextclade CLI version 1.4.3 the "Private mutations" QC check was incorrectly counting individual deletions, rather than contiguous ranges of deletions, as it was before that. This resulted in QC score being too high for sequences that have many deletions. In this version we ensure again that the deletion ranges are counted. This should now bring the "Private mutations" QC score back to what is expected.

Scientific Software - Peer-reviewed - Rust
Published by ivan-aksamentov over 4 years ago

Nextclade - 1.4.4

Nextclade CLI 1.4.4 (2021-11-01)

This is a bugfix release for Nextclade CLI.

[Fix] Prevent Nextclade CLI failing with error "Library not loaded"

The mistake in the Nextclade CLI build was fixed and now it should not look for external libraries on macOS.

Scientific Software - Peer-reviewed - Rust
Published by ivan-aksamentov over 4 years ago

Nextclade - 1.4.3

Nextclade Web 1.7.2, Nextclade CLI 1.4.3 (2021-11-01)

This is a bugfix release for Nextclade Web and Nextclade CLI.

[Fix] Properly display private aminoacid mutations on the tree

This release ensures that both nucleotide and aminoacid mutations on the branches of the phylogenetic tree leading to the nodes representing analyzed sequences are properly displayed and that the corresponding information is correctly written to the output tree JSON. Similarly to how it's done in the main Nextstrain project, these mutations are private, i.e. called relative to the parent node.

The internal reorganization of the code responsible for finding private mutations might also make Nextclade slightly faster and to consume less memory.

Scientific Software - Peer-reviewed - Rust
Published by ivan-aksamentov over 4 years ago

Nextclade - 1.4.2

Nextclade CLI 1.4.2 (2021-10-26)

This is a small bugfix release and only affects Nextclade CLI. Nextclade Web and Nextalign CLI are unchanged.

[Fix] Crash in dataset list command on macOS

Nextclade CLI could sometimes crash on macOS when issued a dataset list command due to an internal error. This was now fixed.

[Fix] Uninformative error message when QC config is missing

When both --input-dataset and --input-qc-config flags are omitted Nextclade CLI now produces a more informative error message, as was intended. Thanks Peter Menzel (@pmenzel) for the report.

Scientific Software - Peer-reviewed - Rust
Published by ivan-aksamentov over 4 years ago

Nextclade - 1.4.1

Nextclade Web 1.7.1, Nextclade CLI 1.4.1 (2021-10-05)

[Fix] Format of CSV/TSV output files

We fixed a few mistakes in CSV and TSV output files, such as missing last delimiter when the "errors" column is empty, inconsistent application of quotation marks and incorrect numeric formats - decimals when integers should be.

Scientific Software - Peer-reviewed - Rust
Published by ivan-aksamentov over 4 years ago

Recent Releases of Nextclade

Nextclade - 3.16.0

3.16.0

Introduce JSON Schema definitions

Implement amino acid mutation labels

Nextclade - 3.15.3

3.15.3

fix: ensure GFF3 fields are correctly percent-encoded and decoded

Nextclade - 3.15.2

3.15.2

fix: calculate phenotypes even if there's no tree

fix: collapse -0.0 to 0.0 in phenotype values

fix: ensure CSV column and category selection is additive

fix: ensure canonical order of CSV columns

Nextclade - 3.15.1

3.15.1

Nextclade Web: fix empty results table

Nextclade - 3.15.0

3.15.0

Nextclade Web: fix country colorings in output tree json #1646

CDS coverage #1514

Nextclade - 3.14.5

3.14.5

Nextclade Web: disable "Relative to" dropdown when dataset has no reference tree

Nextclade - 3.14.4

3.14.4

Fix seed coverage calculation for short references

Nextclade Web: fix crash when using ?multi-dataset URL parameter

Nextclade Web: workaround double run

Nextclade - 3.14.3

3.14.3

Fix dataset suggestions and sorting for short references

Nextclade - 3.14.2

3.14.2

Nextclade Web: crash with custom Auspice JSON dataset

Nextclade - 3.14.1

3.14.1

Nextclade Web: crash with custom datasets

Nextclade - 3.14.0

3.14.0

Nextclade Web: multi-dataset mode

Nextclade Web: add "Download SVG" button to "Tree" page

Nextclade Web: add "Focus on selected" toggle on "Tree" page

Nextclade CLI: global dataset search mode for sort command

Nextclade CLI: fix panics

Nextclade CLI: fix console color mode handling

Nextclade - 3.13.3

3.13.3

Fix crash when exporting annotations for sequences with missing genes

Nextclade - 3.13.2

3.13.2

Speed up Nextclade web, fix crash when using files >45MB on Chromium v136 browsers

Nextclade - 3.13.1

3.13.1

Fix crash on empty query annotations

Nextclade - 3.13.0

3.13.0

Output genome annotations

Nextclade - 3.12.0

3.12.0

Forbid reference sequences with gaps

Nextclade - 3.11.0

3.11.0

Alignment presets

Fix crash with empty reference sequence

Nextclade - 3.10.2

3.10.2

Correctly handle comments in GFF3 files

[cli] Fix verbosity CLI arguments

Nextclade - 3.10.1

3.10.1

[web] Fetch custom inputs from URLs using correct "Accept" HTTP header

Nextclade - 3.9.1

Nextclade 3.9.1

Fix: clade mismatch between placed node and parent node

Nextclade - 3.9.0

Nextclade 3.9.0

Nextclade CLI: Obtain CA certificates from platform trust store; add NEXTCLADE_EXTRA_CA_CERTS / --extra-ca-certs

Update Auspice tree visualization to 2.58.0

Nextclade - 3.8.2

Nextclade Web: fix crash when using `?multi-dataset` URL parameter

Nextclade CLI: global dataset search mode for `sort` command

Nextclade CLI: Obtain CA certificates from platform trust store; add `NEXTCLADE_EXTRA_CA_CERTS` / `--extra-ca-certs`

Allow `index` and `seqName` in column selection

Make reference tree node attribute `clade_membership` optional

Don't read dataset's `tree.json` and `genome_annotation.gff3` unless they are declared

Fix crash when using `--verbosity` option