autocycler - Autocycler v0.5.2

This release includes: * Performance improvements for Autocycler cluster – faster execution and less RAM usage. * New --min_depth option for Autocycler clean * Bash pipeline now includes a time limit on assembly jobs (thanks, @muntean-alex)

Tarballs of pre-built executable binaries are attached: * Linux: * autocycler-linux-x86_64-musl-v0.5.2.tar.gz: x86-64 processors, musl C standard library * autocycler-linux-x86_64-gnu-v0.5.2.tar.gz: x86-64 processors, glibc C standard library * I recommend trying the musl version first, as it's more portable. However, if you encounter a memory allocation crash, then try the gnu version. * Macs: * autocycler-macos-x86_64-v0.5.2.tar.gz: x86-64 Intel processors * autocycler-macos-aarch64-v0.5.2.tar.gz: Apple silicon processors

An HTML copy of the Autocycler docs at the time of release is also attached: autocycler-documentation-v0.5.2.tar.gz

- Rust
Published by rrwick 7 months ago

autocycler - Autocycler v0.5.1

Just a few additions/fixes in this release: * Added hifiasm to Autocycler helper. * Added a new header hint: autocycler_ignore * Fixed error in Dockerfile (thanks, @ppenev-eligo)

Tarballs of pre-built executable binaries are attached: * Linux: * autocycler-linux-x86_64-musl-v0.5.1.tar.gz: x86-64 processors, musl C standard library * autocycler-linux-x86_64-gnu-v0.5.1.tar.gz: x86-64 processors, glibc C standard library * I recommend trying the musl version first, as it's more portable. However, if you encounter a memory allocation crash, then try the gnu version. * Macs: * autocycler-macos-x86_64-v0.5.1.tar.gz: x86-64 Intel processors * autocycler-macos-aarch64-v0.5.1.tar.gz: Apple silicon processors

An HTML copy of the Autocycler docs at the time of release is also attached: autocycler-documentation-v0.5.1.tar.gz

- Rust
Published by rrwick 7 months ago

autocycler - Autocycler v0.5.0

The main change in v0.5.0 is that the helper scripts have now been integrated into Autocycler as a built-in subcommand: * Instead of running canu.sh, you now run autocycler helper canu. * This simplifies installation – no more copying Bash/Python scripts. * The new autocycler helper command also adds features: * Support for Myloasm. * Support for different read types (e.g. PacBio HiFi). * Better cleanup of empty assemblies that could break pipelines. * Per-contig read depths where possible, with filtering options. * Output .log files when produced by the assembler

Other updates: * Fixed bug with passing_clusters column in clustering.tsv file (thanks, @MrTomRod). * Added new columns to clustering.tsv for contig header hints.

Tarballs of pre-built executable binaries are attached: * Linux: * autocycler-linux-x86_64-musl-v0.5.0.tar.gz: x86-64 processors, musl C standard library * autocycler-linux-x86_64-gnu-v0.5.0.tar.gz: x86-64 processors, glibc C standard library * I recommend trying the musl version first, as it's more portable. However, if you encounter a memory allocation crash, then try the gnu version. * Macs: * autocycler-macos-x86_64-v0.5.0.tar.gz: x86-64 Intel processors * autocycler-macos-aarch64-v0.5.0.tar.gz: Apple silicon processors

an HTML copy of the Autocycler docs at the time of release is also attached: autocycler-documentation-v0.5.0.tar.gz

The Autocycler demo data has not changed, so it can be downloaded from the v0.1.0 release.

- Rust
Published by rrwick 8 months ago

autocycler - Autocycler v0.4.0

This release contains: * Added ways to influence Autocycler via input contig headers. * Autocycler cluster terminal output now shows topology information, to show which contigs are circular vs linear. * A new Plassembler helper script, which can help to recover small plasmids that other long-read assemblers often miss. * Updated my full Autocycler pipeline to use Plassember and the new input contig headers. Also limits threads to 128 to prevent Flye from crashing (thanks @samlipworth).

Tarballs of pre-built executable binaries are attached: * Linux: * autocycler-linux-x86_64-musl-v0.4.0.tar.gz: x86-64 processors, musl C standard library * autocycler-linux-x86_64-gnu-v0.4.0.tar.gz: x86-64 processors, glibc C standard library * I recommend trying the musl version first, as it's more portable. However, if you encounter a memory allocation crash, then try the gnu version. * Macs: * autocycler-macos-x86_64-v0.4.0.tar.gz: x86-64 Intel processors * autocycler-macos-aarch64-v0.4.0.tar.gz: Apple silicon processors

There are also some tarballs with cross-platform supporting files: * autocycler-documentation-v0.4.0.tar.gz: an HTML copy of the Autocycler docs at the time of release * autocycler-helper-scripts-v0.4.0.tar.gz: Autocycler's assembly helper scripts

The Autocycler demo data has not changed, so it can be downloaded from the v0.1.0 release.

- Rust
Published by rrwick 10 months ago

autocycler - Autocycler v0.3.0

This release contains: * A new gfa2fasta command for converting Autocycler graphs to FASTA format. * A fix for compatibility with BandageNG (see #17). * Changed terminology for linear sequences: 'open' instead of 'blunt' for non-hairpin ends. This is because 'blunt' might imply a lack of overhang, which is not necessarily true, so 'open' is a more general term.

Tarballs of pre-built executable binaries are attached: * Linux: * autocycler-linux-x86_64-musl-v0.3.0.tar.gz: x86-64 processors, musl C standard library * autocycler-linux-x86_64-gnu-v0.3.0.tar.gz: x86-64 processors, glibc C standard library * I recommend trying the musl version first, as it's more portable. However, if you encounter a memory allocation crash, then try the gnu version. * Macs: * autocycler-macos-x86_64-v0.3.0.tar.gz: x86-64 Intel processors * autocycler-macos-aarch64-v0.3.0.tar.gz: Apple silicon processors

There are also some tarballs with cross-platform supporting files: * autocycler-documentation-v0.3.0.tar.gz: an HTML copy of the Autocycler docs at the time of release * autocycler-helper-scripts-v0.3.0.tar.gz: Autocycler's assembly helper scripts

The Autocycler demo data has not changed, so it can be downloaded from the v0.1.0 release.

- Rust
Published by rrwick 11 months ago

autocycler - Autocycler v0.2.1

This release adds: * The ability to duplicate sequences with the Autocycler clean command. Particularly useful for linear sequences with terminal inverted repeats. * The --max_contigs option to Autocycler compress. Helps to catch bad cases early, so as to not waste time.

Tarballs of pre-built executable binaries are attached: * Linux: * autocycler-linux-x86_64-musl-v0.2.1.tar.gz: Linux systems with x86-64 processors, musl C standard library * autocycler-linux-x86_64-gnu-v0.2.1.tar.gz: Linux systems with x86-64 processors, glibc C standard library * I recommend trying the musl version first, as it's more portable. However, if you encounter a memory allocation crash, then try the gnu version. * Macs: * autocycler-macos-x86_64-v0.2.1.tar.gz: Macs with x86-64 Intel processors * autocycler-macos-aarch64-v0.2.1.tar.gz: Macs with Apple silicon processors

There are also some tarballs with cross-platform supporting files: * autocycler-documentation-v0.2.1.tar.gz: an HTML copy of the Autocycler docs at the time of release * autocycler-helper-scripts-v0.2.1.tar.gz: Autocycler's assembly helper scripts

The Autocycler demo data has not changed, so it can be downloaded from the v0.1.0 release.

- Rust
Published by rrwick about 1 year ago

autocycler - Autocycler v0.2.0

This release adds new functionality to facilitate manual completion of assemblies: * New subcommand: autocycler clean which allows for manual removal of sequences when the consensus assembly is not fully resolved. * Add depth values to consensus_assembly.gfa file (useful for manual cleaning).

Tarballs of pre-built executable binaries are attached: * Linux: * autocycler-linux-x86_64-musl-v0.2.0.tar.gz: Linux systems with x86-64 processors, musl C standard library * autocycler-linux-x86_64-gnu-v0.2.0.tar.gz: Linux systems with x86-64 processors, glibc C standard library * I recommend trying the musl version first, as it's more portable. However, if you encounter a memory allocation crash, then try the gnu version. * Macs: * autocycler-macos-x86_64-v0.2.0.tar.gz: Macs with x86-64 Intel processors * autocycler-macos-aarch64-v0.2.0.tar.gz: Macs with Apple silicon processors

There are also some tarballs with cross-platform supporting files: * autocycler-documentation-v0.2.0.tar.gz: an HTML copy of the Autocycler docs at the time of release * autocycler-helper-scripts-v0.2.0.tar.gz: Autocycler's assembly helper scripts

The Autocycler demo data has not changed, so it can be downloaded from the v0.1.0 release.

- Rust
Published by rrwick about 1 year ago

autocycler - Autocycler v0.1.2

This release includes some fixes/enhancements in response to feedback from the Autocycler alpha testers: * Added a check to the assembly helper scripts to ensure that the output prefix is writable. * Added a genome-size helper script. * Error messages in helper scripts now print to stderr (not stdout). * Changed the default value of --count for autocycler subsample to match new instructions. * Add a message to the end of the autocycler combine stderr to indicate whether or not the assembly appears to be fully resolved. * Lots of improvements/additions to the documentation.

Tarballs of pre-built executable binaries are attached: * autocycler-linux-x86_64-musl-v0.1.2.tar.gz: for Linux systems with x86-64 processors * autocycler-macos-x86_64-v0.1.2.tar.gz: for Macs with x86-64 Intel processors * autocycler-macos-aarch64-v0.1.2.tar.gz: for Macs with Apple silicon processors

There are also some tarballs with cross-platform supporting files: * autocycler-documentation-v0.1.2.tar.gz: an HTML copy of the Autocycler docs at the time of release * autocycler-helper-scripts-v0.1.2.tar.gz: Autocycler's assembly helper scripts

The Autocycler demo data has not changed, so it can be downloaded from the v0.1.0 release.

- Rust
Published by rrwick about 1 year ago

autocycler - Autocycler v0.1.1

This release includes some fixes/enhancements in response to feedback from the Autocycler alpha testers: * Fixed a bad version number in the environment.yml file for installing long-read assemblers. * Added --max_contigs to Autocycler cluster to catch obviously bad input data that could cause the clustering algorithm to hang. * Improved error messages with empty files. * Created a helper script for the metaMDBG assembler. * Allow suppression of terminal colours with an environment variable. * Additions/refinements to the documentation.

Tarballs of pre-built executable binaries are attached: * autocycler-linux-x86_64-musl-v0.1.1.tar.gz: for Linux systems with x86-64 processors * autocycler-macos-x86_64-v0.1.1.tar.gz: for Macs with x86-64 Intel processors * autocycler-macos-aarch64-v0.1.1.tar.gz: for Macs with Apple silicon processors

There are also some tarballs with cross-platform supporting files: * autocycler-documentation-v0.1.1.tar.gz: an HTML copy of the Autocycler docs at the time of release * autocycler-helper-scripts-v0.1.1.tar.gz: Autocycler's assembly helper scripts

The Autocycler demo data has not changed, so it can be downloaded from the previous release.

- Rust
Published by rrwick over 1 year ago

autocycler - Autocycler v0.1.0

The very first release of Autocycler!

Tarballs of pre-built executable binaries are attached: * autocycler-linux-x86_64-musl-v0.1.0.tar.gz: for Linux systems with x86-64 processors * autocycler-macos-x86_64-v0.1.0.tar.gz: for Macs with x86-64 Intel processors * autocycler-macos-aarch64-v0.1.0.tar.gz: for Macs with Apple silicon processors

There are also some tarballs with cross-platform supporting files: * autocycler-demo-dataset.tar: Autocycler's demo dataset * autocycler-documentation-v0.1.0.tar.gz: an HTML copy of the Autocycler docs at the time of release * autocycler-helper-scripts-v0.1.0.tar.gz: Autocycler's assembly helper scripts

- Rust
Published by rrwick over 1 year ago