metasbt - MetaSBT v0.1.5

@cumbof/metasbt@0.1.5

New features

• unpack can automatically rename an unpacked database with the specified --database input argument;
• update exposes two new arguments --uncertainty and --pruning-threshold to tune the profiling performances.

Fixes

• db correctly downloads the selected database version now;
• unpack is now trimming the whole database structure out up to the database folder so that unpack would eventually work as expected;
• unpack automatically fixes the paths to the bloom filter sketches onced a database is unpacked to a new location, usually different from the one where the database was located at the time of packing it;
• update correctly generates a new database also in case of no new unknown genomes.

- Python
Published by cumbof 8 months ago

metasbt - MetaSBT v0.1.4.post1

@cumbof/metasbt@0.1.4.post1

New object-oriented implementation of MetaSBT. Clusters are consistent with the definition of Average Nucleotide Identity (ANI). Clusters' boundaries are defined as the minimum and maximum ANI distance between all the genomes under a specific cluster.

New features

It provides the following subroutines: - db: List and retrieve public MetaSBT databases; - index: Index a set of reference genomes and build the first baseline of a MetaSBT database; - kraken: Export a MetaSBT database into a custom kraken database; - pack: Build a compressed tarball with a MetaSBT database and report its sha256; - profile: Profile an input genome and report the closest cluster at all the seven taxonomic levels and the closest genome in a MetaSBT database; - sketch: Sketch the input genomes; - summarize: Summarize the content of a MetaSBT database and report some statistics; - test: Check for dependencies and run unit tests. This must be used by code maintainers only; - unpack: Unpack a local MetaSBT tarball database; - update: Update a MetaSBT database with new metagenome-assembled genomes.

The MetaSBT core provides an interface to the Database and Entry class abstractions.

Fixes

None

- Python
Published by cumbof 8 months ago

metasbt - MetaSBT v0.1.3

MetaSBT v0.1.3 brings the following improvements.

New features

• New option --uniform-strand available with the index and update modules for processing the input sequences all on the same strand. Mainly used for viral sequences;
• New option --use-representatives available with the index module to use only three representative genomes at the species level;
• New option --resume available with the index and update modules able to resume the index and update processes in case of unexpected errors;
• New expand_fasta.py utility in scripts to expand input fasta files into multiple file. One fasta file for each read. Mainly used for viral sequences;
• New fastcluster.py utility in script to compute a average-linkage hierarchical clustering of a set of genomes based on their Mash distances;
• Both the index and update modules now display a worning message in case the configuration file under --resume has been previously generated with a different version of MetaSBT;
• Both the index and update modules now integrate CheckV and EukCC for assessing the quality of viruses and eukaryotes;
• CheckM has been upgraded to CheckM2;
• The cluster() function in utils is now running in parallel;
• The howdesbt bfdistance command for computing the distances between bloom filters is now running in parallel.

Fixes

• It correctly checks now for new framework versions when starting a new metasbt instance;
• Fixed genome quality filtering on completeness and contamination during the update;
• Improving docstring adopting the numpydoc documentation format.

- Python
Published by cumbof over 1 year ago

metasbt - MetaSBT v0.1.2

First public stable release of MetaSBT.

It is composed of the following modules:

• index: build a MetaSBT database by building a series of Sequence Bloom Trees at different taxonomic levels;
• boundaries: define taxonomy-specific boundaries as the minimum and maximum number of kmers in common between all the genomes under a specific cluster;
• profile: taxonomically profile a genome by querying a MetaSBT database at different taxonomic levels;
• report: build a report table describing the content of a MetaSBT database;
• update: update a MetaSBT database with new genomes;
• tar: pack a MetaSBT database into a ready-to-be-distributed tarball;
• install: install a MetaSBT database tarball locally under a specific location of the file system.

The framework also comes with a set of utilities:

• bf_sketch.py: build minimal bloom filter sketches with cluster-specific marker kmers;
• esearch_txid.sh: retrieve GCAs from NCBI GenBank given a specific taxonomic ID;
• get_ncbi_genomes.py: retrieve reference genomes and metagenome-assembled genomes under a specific superkingdom and kingdom from NCBI GenBank;
• howdesbt_index.sh: index genomes with HowDeSBT;
• uniform_inputs.sh: uniform input genome files extension.

- Python
Published by cumbof almost 3 years ago