emmtyper is a command-line tool for in silico emm-typing of Streptococcus pyogenes using de novo or complete genome assemblies. It utilizes the U.S. Centers for Disease Control and Prevention (CDC) curated trimmed emm subtype database to classify emm genes while distinguishing them from homologous genes (enn and mrp). The tool operates in two modes: BLAST, where contigs are directly matched against the CDC database, and PCR, where in silico PCR is performed before BLAST analysis. Users can choose between canonical CDC primers or an alternative primer set from Frost et al. (2020), with the option to provide custom primers. By efficiently identifying and classifying emm genes, emmtyper supports epidemiological surveillance and molecular characterization of S. pyogenes infections.
Tags: emm typing, Streptococcus pyogenes, cpg
Open emmtyper in the CPG Portal. Configuring and running a tool needs JavaScript.