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/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 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