modules/staramr_search
Scans genome contigs against the ResFinder, PlasmidFinder, and PointFinder databases.
Output
A summary of all detected AMR genes/mutations/plasmids/sequence type in each genome, one genome per line.
A series of descriptive statistics is also provided for each genome,
as well as feedback for whether or not the genome passes several quality metrics and if not,
feedback on why the genome fails.
*_results/summary.tsv A summary of all detected AMR genes/mutations/plasmids/sequence type in each genome, one genome per line.
A series of descriptive statistics is also provided for each genome,
as well as feedback for whether or not the genome passes several quality metrics and if not,
feedback on why the genome fails.
*_results/detailed_summary.tsv A tabular file of each AMR gene and additional BLAST information from the ResFinder database, one gene per line.
*_results/resfinder.tsv A tabular file of each AMR plasmid type and additional BLAST information from the PlasmidFinder database, one plasmid type per line.
*_results/plasmidfinder.tsv A tabular file of each multi-locus sequence type (MLST) and it’s corresponding locus/alleles, one genome per line.
*_results/mlst.tsv The command-line, database versions, and other settings used to run staramr.
*_results/settings.txt An optional tabular file of each AMR point mutation and additional BLAST information from the PointFinder database, one gene per line.
*_results/pointfinder.tsv maintainer
