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dc.contributor.authorWaters, Nicholas R.
dc.contributor.authorAbram, Florence
dc.contributor.authorBrennan, Fiona
dc.contributor.authorHolmes, Ashleigh
dc.contributor.authorPritchard, Leighton
dc.date.accessioned2021-02-17T17:50:54Z
dc.date.available2021-02-17T17:50:54Z
dc.date.issued2020-09-01
dc.identifier.citationWaters, N. R., Abram, F., Brennan, F., Holmes, A., Pritchard, L. Easy phylotyping of Escherichia coli via the EzClermont web app and command-line tool. Access Microbiology. 2020, 9 (2). doi: https://doi.org/10.1099/acmi.0.000143en_US
dc.identifier.urihttp://hdl.handle.net/11019/2389
dc.descriptionpeer-revieweden_US
dc.description.abstractThe Clermont PCR method for phylotyping Escherichia coli remains a useful classification scheme even though genome sequencing is now routine, and higher-resolution sequence typing schemes are now available. Relating present-day whole-genome E. coli classifications to legacy phylotyping is essential for harmonizing the historical literature and understanding of this important organism. Therefore, we present EzClermont – a novel in silico Clermont PCR phylotyping tool to enable ready application of this phylotyping scheme to whole-genome assemblies. We evaluate this tool against phylogenomic classifications, and an alternative software implementation of Clermont typing. EzClermont is available as a web app at www.ezclermont.org, and as a command-line tool at https://nickp60.github.io/EzClermont/.en_US
dc.language.isoenen_US
dc.publisherMicrobiology Societyen_US
dc.relation.ispartofseriesAccess Microbiology;
dc.rightsAttribution-ShareAlike 4.0 International*
dc.rights.urihttp://creativecommons.org/licenses/by-sa/4.0/*
dc.subjectphylogroups web appen_US
dc.subjectclassificationen_US
dc.subjectbioinformaticsen_US
dc.subjectgenomicsen_US
dc.subjectEscherichia colien_US
dc.titleEasy phylotyping of Escherichia coli via the EzClermont web app and command-line toolen_US
dc.typeArticleen_US
dc.identifier.doihttps://doi.org/10.1099/acmi.0.000143
dc.contributor.sponsorThe James Hutton Instituteen_US
dc.contributor.sponsorNational University of Ireland, Galwayen_US
dc.source.volume2
dc.source.issue9
refterms.dateFOA2021-02-17T17:50:55Z
dc.source.journaltitleAccess Microbiology


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