PLEASE NOTE: THIS SCRIPT IS DEPRECATED. WE RECOMMEND THE USE OF ARIBA (https://github.com/sanger-pathogens/ariba) INSTEAD.
A python script for identifying matches to resistance alleles in genome assemblies. Unlike many other methods map_resistome will highlight partial matches at contig boundaries that may be the result of assembly issues for repetitive resistance genes.
Requirements:
Requires local intallations of SMALT and samtools. If these are not in your default PATH, please edit the SMALT_DIR and SAMTOOLS_DIR locations in the two python files.
Usage: map_resistome.py [options]
Options:
--version show program's version number and exit
-h, --help show this help message and exit
-c FILE, --contigs=FILE multifasta containing contigs to search in
-f FILE, --forward=FILE forward fastq file (may be zipped, but must end .gz)
-r FILE, --reverse=FILE
reverse fastq file (may be zipped, but must end .gz)
-g FILE, --genes=FILE
multifasta containing genes to search for
-o FILE, --output=FILE
output prefix
-i float, --id=float minimum id to report match (excluding clipping due to
contig breaks). Must be between 0 and 1. [default =
0.9]