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TBProfiler v4.0.0
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@jodyphelan jodyphelan released this 04 Nov 15:03
· 498 commits to master since this release
v4.0.0
b648e4b

Changes

The json result files are formatted slightly differently from previous versions to accommodate the changes detailed below. As a consequence, operations such as collate will not work on results from previous versions.

  • Switching to snpEff for consequence prediction for full HGVS compliance
  • Optional use of suspect-BDQ and suspect-PZA for prediction of resistance
  • Switching over to new Pre-XDR and XDR definitions (see WHO page)
  • Allowing user-specified non drug resistance annotations (e.g. phylogenetic or compensatory mutations)
  • Annotation of multiple consequences which is useful for overlapping promoter/coding regions
  • Improvements in nanopore variant calling speed by moving to freebayes.
  • Adding median coverage (#178)
  • More flexible reference name matching when creating database
  • Make freebayes the default variant caller
  • Add some colour to terminal output!
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