New PGAP release: Structural and functional annotation improvements

A new version of the Prokaryotic Genome Annotation Pipeline (PGAP) is available on GitHub. With this release, you can expect:

  • Incremental improvements in structural annotation, driven by increased weight of GeneMarkS2+ ab initio models at loci with only weak evidence, such as low identity and low coverage protein alignments or partial HMM signatures.
  • Better structural annotation and more specific functional annotation as a result of the incorporation of PFAM 34 and extensive curation of HMMs, BlastRules and Conserved Domain architectures by NCBI experts.
  • Fewer overly stringent calls by the taxonomy verification module for several species, including the human pathogens Listeria monocytogenes, Campylobacter lari, and Vibrio vulnificus. This is a result of manual review and adjustment of the minimum percent identity thresholds used by the Average Nucleotide Identity tool.
  • Multiple bug fixes. Notably, users of Azure Debian 10 machines can now run PGAP successfully, as we have incorporated GeneMarkS2+ compiled under Linux kernel 3 into the PGAP image.

Please try this release and send us your feedback!

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