RT Journal Article
SR Electronic
T1 Easily phylotyping <em>E. coli</em> via the EzClermont web app and command-line tool
JF bioRxiv
FD Cold Spring Harbor Laboratory
SP 317610
DO 10.1101/317610
A1 Waters, Nicholas R.
A1 Abram, Florence
A1 Brennan, Fiona
A1 Holmes, Ashleigh
A1 Pritchard, Leighton
YR 2018
UL http://biorxiv.org/content/early/2018/05/09/317610.abstract
AB 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.ieSupplementary information Table S1: test dataset; S2: validation dataset; S3: results.