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)

Research output: Contribution to journalArticlepeer-review

24 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 languageEnglish
Article number000143
Number of pages5
JournalAccess Microbiology
Volume2
Issue number9
DOIs
Publication statusPublished - 19 Jun 2020

Keywords

  • ECOR, Escherichia coli Reference Collection
  • MLST, multilocus sequence typing

Fingerprint Dive into the research topics of 'Easy phylotyping of Escherichia coli via the EzClermont web app and command-line tool'. Together they form a unique fingerprint.

Cite this