emmtyper

emmtyper is a command line tool for emm-typing of Streptococcus pyogenes using a de novo or complete assembly. By default, we use the U.S. Centers for Disease Control and Prevention trimmed emm subtype database, which can be found here (https://www2a.cdc.gov/ncidod/biotech/strepblast.asp). The database is curated by Dr. Velusamy Srinivasan. Inner workings The difficulty in performing M-typing is that there is a single gene of interest (emm), but two other homologue genes (enn and mrp), often referred to as emm-like. The homologue genes may or may not occur in the isolate of interest. When performing emm-typing from an assembly, we can distinguish betweeen one or more clusters of matches on the contigs. The best match for each of the clusters identified is then parsed from the BLAST results. Where possible, we try to distinguish between matches to the emm gene, and matches to one of the emm-like genes.