Easy phylotyping of Escherichia coli via the EzClermont web app and command-line tool
dc.contributor.author | Waters, Nicholas R. | |
dc.contributor.author | Abram, Florence | |
dc.contributor.author | Brennan, Fiona | |
dc.contributor.author | Holmes, Ashleigh | |
dc.contributor.author | Pritchard, Leighton | |
dc.date.accessioned | 2021-02-17T17:50:54Z | |
dc.date.available | 2021-02-17T17:50:54Z | |
dc.date.issued | 2020-09-01 | |
dc.identifier.citation | Waters, 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.0.000143 | en_US |
dc.identifier.uri | http://hdl.handle.net/11019/2389 | |
dc.description | peer-reviewed | en_US |
dc.description.abstract | The 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.iso | en | en_US |
dc.publisher | Microbiology Society | en_US |
dc.relation.ispartofseries | Access Microbiology; | |
dc.rights | Attribution-ShareAlike 4.0 International | * |
dc.rights.uri | http://creativecommons.org/licenses/by-sa/4.0/ | * |
dc.subject | phylogroups web app | en_US |
dc.subject | classification | en_US |
dc.subject | bioinformatics | en_US |
dc.subject | genomics | en_US |
dc.subject | Escherichia coli | en_US |
dc.title | Easy phylotyping of Escherichia coli via the EzClermont web app and command-line tool | en_US |
dc.type | Article | en_US |
dc.identifier.doi | https://doi.org/10.1099/acmi.0.000143 | |
dc.contributor.sponsor | The James Hutton Institute | en_US |
dc.contributor.sponsor | National University of Ireland, Galway | en_US |
dc.source.volume | 2 | |
dc.source.issue | 9 | |
refterms.dateFOA | 2021-02-17T17:50:55Z | |
dc.source.journaltitle | Access Microbiology |