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Releases: cumbof/MetaSBT

MetaSBT v0.1.3

28 Jun 09:31
@cumbof cumbof
0.1.3
d8989ec
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MetaSBT v0.1.3 Latest
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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.
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MetaSBT v0.1.2

16 May 19:07
@cumbof cumbof
0.1.2
d7f416d
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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.
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