Loading...
Easy phylotyping of Escherichia coli via the EzClermont web app and command-line tool
Waters, Nicholas R. Abram, Florence Brennan, Fiona Holmes, Ashleigh Pritchard, Leighton
Waters, Nicholas R.
Abram, Florence
Brennan, Fiona
Holmes, Ashleigh
Pritchard, Leighton
Citations
Altmetric:
Date
2020-09-01
Collections
Files
Loading...
main article
Adobe PDF, 1.71 MB
Research Projects
Organizational Units
Journal Issue
Citation
Waters, N. R., Abram, F., Brennan, F., Holmes, A., Pritchard, L. Easy phylotyping of Escherichia coli via the EzClermont web app and command-line tool. Access Microbiology. 2020, 9 (2). doi: https://doi.org/10.1099/acmi.0.000143
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/.