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AMRFinderPlus v3.11.11
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@evolarjun evolarjun released this 18 Apr 12:56
· 129 commits to master since this release
amrfinder_v3.11.11
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Learn about vigilant mode.

This release has two primary changes

  1. Version checking for blast on Mac to avoid the bug in BLAST 2.12.0 with the -mt_mode parameter
  2. Updated handling of special characters in the sequence identifiers in GFF and FASTA files.

Special character handling

Implemented special character handling in GFF files according to https://github.com/The-Sequence-Ontology/Specifications/blob/master/gff3.md. The following need to be escaped in the sequence identifiers using URL-style codes in .gff files:

  • # (comment start)
  • tab (%09)
  • newline (%0A)
  • carriage return (%0D)
  • % percent (%25)
  • control characters (%00 through %1F, %7F)
  • ; semicolon (%3B)
  • = equals (%3D)
  • & ampersand (%26)
  • , comma (%2C)

Added input checking for nucleotide sequences because 'makeblastdb' truncates and/or alters sequence identifiers with the following characteristics. Now nucleotide FASTA identifiers (characters after '>' and before the first whitespace) with any of the following will cause amrfinder to exit with an error message.

  • FASTA identifier starts with '?'
  • FASTA identifier contains the two character sequence ',,' or '\t' (the character '\' followed by the character 't')
  • FASTA identifier ends with ';' '~' ',' or '.'

Bug fix for Bioconda compatibility

On Mac the BLAST parameter -mt_mode requires BLAST version 2.13.0 to run on short query sequences.

This release includes a bug-fix to allow AMRFinderPlus to be compatible with Bioconda which doesn't have BLAST+ version 2.13.0 for the Mac. The previous release 3.11.8 could not be added to Bioconda because at the time of release Bioconda did not have BLAST+ version 2.13.0 for Mac.

See also release notes for version 3.10.8: https://github.com/ncbi/amr/releases/tag/amrfinder_v3.11.8

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