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

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

Posted 09 May 2018
bioRxiv DOI: 10.1101/317610

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 <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. Contact n.waters4{at}nuigalway.ie, leighton.pritchard{at}strath.ac.uk Supplementary information Table S1: test dataset; S2: validation dataset; S3: results.

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