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.