Easy phylotyping of Escherichia 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

Easy phylotyping of Escherichia coli via the EzClermont web app and command-line tool

Nicholas R. Waters, Florence Abram, Fiona Brennan, Ashleigh Holmes, Leighton Pritchard (Lead / Corresponding author)

DArcy Thompson Unit

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

68 Downloads (Pure)

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/.

Original language	English
Article number	000143
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

ECOR, Escherichia coli Reference Collection
MLST, multilocus sequence typing

Access to Document

10.1099/acmi.0.000143Licence: CC BY

Final Published VersionFinal published version, 1.71 MBLicence: CC BY

Cite this

@article{e1c31d8910cf4bd7bb060b492de88684,

title = "Easy phylotyping of Escherichia coli via the EzClermont web app and command-line tool",

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/.",

keywords = "ECOR, Escherichia coli Reference Collection, MLST, multilocus sequence typing",

author = "Waters, {Nicholas R.} and Florence Abram and Fiona Brennan and Ashleigh Holmes and Leighton Pritchard",

note = "{\textcopyright} 2020 The Authors.",

year = "2020",

month = jun,

day = "19",

doi = "10.1099/acmi.0.000143",

language = "English",

volume = "2",

journal = "Access Microbiology",

issn = "2516-8290",

publisher = "Microbiology Society",

number = "9",

}

TY - JOUR

T1 - Easy phylotyping of Escherichia coli via the EzClermont web app and command-line tool

AU - Waters, Nicholas R.

AU - Abram, Florence

AU - Brennan, Fiona

AU - Holmes, Ashleigh

AU - Pritchard, Leighton

PY - 2020/6/19

Y1 - 2020/6/19

N2 - 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/.

AB - 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/.

KW - ECOR, Escherichia coli Reference Collection

KW - MLST, multilocus sequence typing

U2 - 10.1099/acmi.0.000143

DO - 10.1099/acmi.0.000143

M3 - Article

C2 - 33195978

SN - 2516-8290

VL - 2

JO - Access Microbiology

JF - Access Microbiology

IS - 9

M1 - 000143

ER -

Easy phylotyping of Escherichia coli via the EzClermont web app and command-line tool

Abstract

Keywords

Access to Document

Fingerprint

Cite this