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@jvhagey jvhagey released this 04 Jun 20:48
· 43 commits to main since this release
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v2.3.1
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v2.3.1 (06/04/2026)

Full Changelog

Database Updates:

  • ANI REFSEQ database: 20260521
  • MLST : 20260603

Implemented Enhancements:

  • Added Alerts column to Terra.bio output to be in line with the rest of PHX output.

Fixed Bugs:

  • Fixed bug that caused failure for when Shigella spp is identified issue 210.
  • Fixed bug that caused failure on Terra.bio at PROKKA step issue 209.
  • Fixed bug that caused warning counts to be off on Terra.bio issue 211.
  • Added Alerts column to Terra.bio output to be in line with the rest of PHX output.
  • Fixed bug that resulted in failed lookups for taxa with parentheses and, in some cases, 'sp.' in the NCBI_Assembly_Stats file. Improved determine_taxa_id.py lookup handling and adjusted how parentheses are handled during ANI database creation
  • MLST Fixes:
    • Fixed issue with vcholorae's 2nd scheme being pointed to the wrong folder (non-existent).
  • GRiPHin Fixes:
    • Fixed bug that caused NA to disappear from Stdev column, which would then skip the warning that there were <10 references for ratio and gc calculations.
    • Fixed bug that cut off text after sp. in Kraken2 output.
    • Fixed bug causing some BIG-5 genes to not be highlighted correctly (example blaOXA-23).
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