AMRFinderPlus - Identify AMR genes and point mutations, and virulence and stress resistance genes in assembled bacterial nucleotide and protein sequence.
Added input checking for nucleotide sequences because 'makeblastdb' truncates and/or alters sequence identifiers with the following characteristics:
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 to allow amrfinderplus to be compatible with bioconda which doesn't have BLAST+ version 2.13.0 for the Mac. Previous release 3.11.8 (PD-4552) could not be added to bioconda.
Implemented special character handling in .gff files according to https://github.com/The-Sequence-Ontology/Specifications/blob/master/gff3.md
Added input checking for nucleotide sequences because 'makeblastdb' truncates and/or alters sequence identifiers with the following characteristics:
Bug-fix to allow amrfinderplus to be compatible with bioconda which doesn't have BLAST+ version 2.13.0 for the Mac. Previous release 3.11.8 (PD-4552) could not be added to bioconda.
See also release notes for version 3.10.8: https://github.com/ncbi/amr/releases/tag/amrfinder_v3.11.8, PD-4557, and PD-3918
On Mac the BLAST parameter -mt_mode requires BLAST version 2.13.0