Changelog

Version 0.1.4

New kraken.py utility in scripts to create custom kraken2 databases with MetaSBT taxonomic labels;
The tar and install commands have been replaced with the pack.sh and unpack.sh utilities in scripts.

Clusters' boundaries are now defined as the minimum and maximum Average Nucleotide Identity (ANI) between all the genomes under a specific cluster.

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.