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Predict resistance to HIV drugs, include ambiguous consensus
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@ozagordi ozagordi released this 06 Feb 13:49
· 34 commits to master since this release
v2.2
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ozagordi Osvaldo Zagordi
GPG key ID: 16B13DF8774B49B3
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This release of MinVar includes several changes and a couple of important updates.

The most important is that, when running on HIV, sierrapy
is used to interrogate HIVdb and obtain prediction of resistance to drugs.

The report also includes ambiguity scores (fraction of ambiguous nucleotides), a measure useful to
estimate the time of infection.

Further, a consensus sequence with wobble bases is now part of the output.

Added

  • Report now includes ambiguity score derived from ambiguous consensus sequence.
  • Consensus sequence with ambiguous bases is saved into cns_ambiguous.fasta.
  • Cells of drug resistance report are colour coded.
  • The report includes levels of drug resistance inferred by HIVdb.

Changed

  • Recombinant sequences are checked for also with HIV data.
  • Threshold for sierra is read from the INI file ~/.minvar/runpars.ini
  • Minor changes in final report.
  • masterComments files with DRMs lists are updated to version 8.4
  • Both full drug name and abbreviation are written.
  • Subtype inference only reports top hit, subtype names are now clearer.
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