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

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

doi:10.1099/acmi.0.000143

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

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

Strathclyde Institute Of Pharmacy And Biomedical Sciences

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Abstract

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.

Original language	English
Number of pages	5
Journal	Access Microbiology
Volume	2
Issue number	9
DOIs	https://doi.org/10.1099/acmi.0.000143
Publication status	Published - 19 Jun 2020

Keywords

Escherichia coli
phylotyping
geno ics
bioinformatics

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10.1099/acmi.0.000143Licence: CC BY 4.0

Waters-etal-AM-2020-Easily-phylotyping-E-coli-via-the-EzClermont-web-appFinal published version, 1.71 MBLicence: CC BY 4.0

Cite this

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abstract = "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.",

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AU - Holmes, Ashleigh

AU - Pritchard, Leighton

PY - 2020/6/19

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N2 - 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.

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.

KW - Escherichia coli

KW - phylotyping

KW - geno ics

KW - bioinformatics

UR - https://www.microbiologyresearch.org/content/journal/acmi

UR - https://www.microbiologyresearch.org/content/journal/acmi/10.1099/acmi.0.000143

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

Abstract

Keywords

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