Skip to content

2023-05-17.build6771
Compare
Choose a tag to compare
@azat-badretdin azat-badretdin released this 23 May 20:27
· 43 commits to master since this release
2023-05-17.build6771
2388d68

This release is based on PGAP-6.5. It includes the following features and bug fixes:

  • Addition of attributes (Gene Ontology terms, EC numbers, gene symbols) to more protein-coding features, by propagation from curated conserved domain architectures (CDD architectures)
  • Incremental improvements in structural algorithm
  • Addition of simple option for passing fasta and organism to pgap.py via parameters instead of a yaml file. This option is not sufficient and should NOT be used if the annotated assembly is intended for submission to GenBank.
  • Improved help text for pgap.py
  • Bug fixes:
    • for small circular plasmids, elimination of crashes when alignment covers almost all of the sequence of the plasmid
    • consistency of partiality and pseudo-status of features between cdregions and genes
    • fixed CPU handling in SLURM environment
    • use of fasta file name instead of 'gc_assm_name' as assembly name in ani-tax-report files

Third Party Software and Data versions used (no changes since last release):

  • GeneOntology 2023-01-01
  • tRNAscan-SE 2.0.12
  • hmmer v.3.1b2
  • CRISPR v.1.02
  • AntiFam v.3.0
  • Rfam v.14.4
  • GeneMarkS2 v.1.14_1.25
  • infernal v.1.1.1
Assets 2