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:10.1101/317610

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: Working paper

59 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
Place of Publication	Cold Spring Harbor, NY
Number of pages	6
DOIs	https://doi.org/10.1101/317610
Publication status	Published - 31 Dec 2019

Keywords

phylotyping
Escherichia coli
Clermont PCR method

Access to Document

10.1101/317610Licence: CC BY 4.0

Waters-etal-bioRxiv-2019-Easily-phylotyping-E-coli-via-the-EzClermont-web-app-and-command-line-toolFinal published version, 246 KBLicence: CC BY 4.0

2 Article

Easily phylotyping E. coli via the EzClermont web app and command-line tool
Waters, N. R., Abram, F., Brennan, F., Holmes, A. & Pritchard, L., 19 Jun 2020, In: Access Microbiology . 2, 9, 5 p.
Research output: Contribution to journal › Article › peer-review

Open Access
File
35 Downloads (Pure)
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
8 Citations (Scopus)

39 Downloads (Pure)

1 Education Outreach

PhD Supervision
Brennan, F. (Advisor), Abram, F. (Advisor), Pritchard, L. (Advisor), Holmes, A. (Advisor) & Waters, N. R. (Recipient)
1 May 2016 → 31 May 2020
Activity: Public Engagement and Outreach › Education Outreach

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

Fingerprint

Research output

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

riboSeed: leveraging prokaryotic genomic architecture to assemble across ribosomal regions

Activities

PhD Supervision

Cite this