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v1.1 - INSDC submission & annotation of MAGs: Hey! Ho! Let's go

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@oschwengers oschwengers released this 23 Aug 21:33
· 417 commits to main since this release

This is the first minor release (v1.1) introducing several new features, many improvements and countless bug fixes.

Compatible database scheme version: 3 v3.0

New features:

  • add new --compliant option for INSDC genome submissions: #69 (Thanks @michoug)
  • introduce PSCCs (UniRef50) as a fallback if PSCs (UniRef90) are not detected, greatly improving the annotation of less represented species and metagenome-assembled genomes (MAGs): 84c808f
  • export nucleotide sequences: #57 (Thanks @mcroxen)
  • revise suspect CDS product names: f85970b

Improvements:

  • various improvements and fixes in GFF3, GenBank and EMBL files to adhere to INSDC specs: #69
  • improve internal DB download: bdd665a
  • use Diamond version v2.0.11 and its --fast option: c82f4e2 19c95d8 (Thanks to @bbuchfink for bbuchfink/diamond#419)
  • use stable CLI progress library alive-progress 0ac5625
  • improve GFF3 output regarding GFF3 specs: 697121f
  • store AMRFinderPlus DB within the Bakta DB directory: 04ff7b0 (Thanks to @LuisFF)
  • redirect BAKTA-TMP directory to AMRFinderPlus to prevent stale files: 26f81fc
  • detect & mark tmRNA on sequence edges: 782f640
  • adhere to translation table in tmRNA prediction: 450d6b7

Bug fixes: