Easily phylotyping E. coli via the EzClermont web app and command-line tool.

Abstract

The Clermont PCR method of phylotyping Escherichia coli has remained a useful classification scheme despite the proliferation of higher-resolution sequence typing schemes. We have implemented an in silico Clermont PCR method as both a web app and as a command-line tool to allow researchers to easily apply this phylotyping scheme to genome assemblies easily. Availability and ImplementationEzClermont is available as a web app at http://www.ezclermont.org. For local use, EzClermont can be installed with pip or installed from the source code at https://github.com/nickp60/ezclermont. All analysis was done with version 0.4.0. Contactn.waters4@nuigalway.ie, leighton.pritchard@strath.ac.uk Supplementary informationTable S1: test dataset; S2: validation dataset; S3: results.