Changelog

Version 0.1.3

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.

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.

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.