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

Nicholas R. Waters; Florence Abram; Fiona Brennan; Ashleigh Holmes; Leighton Pritchard

doi:10.1101/317610

Summary

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 Implementation EzClermont is available as a web app at https://nickp60.pythonanywhere.com. For local use, Ez-Clermont 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.

Contact n.waters4{at}nuigalway.ie

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