Cargando…
Easy phylotyping of Escherichia coli via the EzClermont web app and command-line tool
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...
Autores principales: | , , , , |
---|---|
Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Microbiology Society
2020
|
Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7656184/ https://www.ncbi.nlm.nih.gov/pubmed/33195978 http://dx.doi.org/10.1099/acmi.0.000143 |
_version_ | 1783608329090629632 |
---|---|
author | Waters, Nicholas R. Abram, Florence Brennan, Fiona Holmes, Ashleigh Pritchard, Leighton |
author_facet | Waters, Nicholas R. Abram, Florence Brennan, Fiona Holmes, Ashleigh Pritchard, Leighton |
author_sort | Waters, Nicholas R. |
collection | PubMed |
description | 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/. |
format | Online Article Text |
id | pubmed-7656184 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2020 |
publisher | Microbiology Society |
record_format | MEDLINE/PubMed |
spelling | pubmed-76561842020-11-12 Easy phylotyping of Escherichia coli via the EzClermont web app and command-line tool Waters, Nicholas R. Abram, Florence Brennan, Fiona Holmes, Ashleigh Pritchard, Leighton Access Microbiol Method 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/. Microbiology Society 2020-06-19 /pmc/articles/PMC7656184/ /pubmed/33195978 http://dx.doi.org/10.1099/acmi.0.000143 Text en © 2020 The Authors http://creativecommons.org/licenses/by/4.0/ This is an open-access article distributed under the terms of the Creative Commons Attribution License. |
spellingShingle | Method Waters, Nicholas R. Abram, Florence Brennan, Fiona Holmes, Ashleigh Pritchard, Leighton Easy phylotyping of Escherichia coli via the EzClermont web app and command-line tool |
title | Easy phylotyping of Escherichia coli via the EzClermont web app and command-line tool |
title_full | Easy phylotyping of Escherichia coli via the EzClermont web app and command-line tool |
title_fullStr | Easy phylotyping of Escherichia coli via the EzClermont web app and command-line tool |
title_full_unstemmed | Easy phylotyping of Escherichia coli via the EzClermont web app and command-line tool |
title_short | Easy phylotyping of Escherichia coli via the EzClermont web app and command-line tool |
title_sort | easy phylotyping of escherichia coli via the ezclermont web app and command-line tool |
topic | Method |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7656184/ https://www.ncbi.nlm.nih.gov/pubmed/33195978 http://dx.doi.org/10.1099/acmi.0.000143 |
work_keys_str_mv | AT watersnicholasr easyphylotypingofescherichiacoliviatheezclermontwebappandcommandlinetool AT abramflorence easyphylotypingofescherichiacoliviatheezclermontwebappandcommandlinetool AT brennanfiona easyphylotypingofescherichiacoliviatheezclermontwebappandcommandlinetool AT holmesashleigh easyphylotypingofescherichiacoliviatheezclermontwebappandcommandlinetool AT pritchardleighton easyphylotypingofescherichiacoliviatheezclermontwebappandcommandlinetool |