Resistance gene detection. (a) Venn diagram of antimicrobial resistance genes detected by SRST2 and assembly?+?BLAST, where the threshold for `detections of a gene is ?90% coverage and ?90% identity with a reference allele. No genes were detected by assembly?+?BLAST but not SRST2. (b) Distribution of average read depths per gene, calculated by SRST2 from mapped reads, for all genes detected by SRST2. (c) Coverage and nucleotide identity (%ID), as calculated by SRST2, for all genes detected by SRST2 but not by assembly?+?BLAST. (d) Impact of lowering the coverage threshold for detection of genes by BLAST (for those genes with ?15 read depth).