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

Research output: Contribution to journal › Article › peer-review

3 Downloads (Pure)

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
Article number	ACMI-D-20-00006
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

Access to Document

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

1 Article
1 Working paper

Easily phylotyping E. coli via the EzClermont web app and command-line tool
Waters, N. R., Abram, F., Brennan, F., Holmes, A. & Pritchard, L., 31 Dec 2019, Cold Spring Harbor, NY, 6 p.
Research output: Working paper

Open Access
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riboSeed: leveraging prokaryotic genomic architecture to assemble across ribosomal regions
Waters, N. R., Abram, F., Brennan, F., Holmes, A. & Pritchard, L., 20 Jun 2018, In: Nucleic Acids Research. 46, 11, 10 p., e68.
Research output: Contribution to journal › Article › peer-review

Open Access
File

2 Citations (Scopus)

5 Downloads (Pure)

1 Other

PhD Supervision
Fiona Brennan (Advisor), Florence Abram (Advisor), Leighton Pritchard (Advisor), Ashleigh Holmes (Advisor) & Nicholas R. Waters (Recipient)
1 May 2016 → 31 May 2020
Activity: Other activity types › Other

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

Abstract

Keywords

Access to Document

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

riboSeed: leveraging prokaryotic genomic architecture to assemble across ribosomal regions

PhD Supervision

Cite this