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MetaSBT v0.1.2
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@cumbof cumbof released this 16 May 19:07
· 74 commits to main since this release
0.1.2
d7f416d

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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