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2022-02-10.build5872
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@azat-badretdin azat-badretdin released this 15 Feb 22:21
· 141 commits to master since this release
2022-02-10.build5872
09774c7

This release is based on PGAP-6.0. It includes the following features and bug fixes:

  • Gene Ontology terms are now added to CDSs and proteins, when known. Like EC numbers, these are propagated from HMMs and BlastRules used to name the proteins.
  • Incorporated 17 RFAM models for the annotation of more riboswitches
  • Introduced the --auto-correct-tax flag in pgap.py, to override the organism provided in the input YAML file, if the taxcheck predicts a different organism with high confidence. Use in combination with the --taxcheck flag
  • Introduced a minimum coverage threshold of 20% to taxcheck  - if the query assembly doesn't match any type assembly over 20%, taxcheck will return inconclusive results (not predict an organism)
  • Added support for Debian 10
  • Bug fix: assemblies for organisms without a genus in their lineage can now be annotated.
  • Bug fix: running PGAP with Singularity without internet access (--no-internet) is now possible. Users need to point pgap.py to a local SIF image (converted from Docker) using the --container-path argument.
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