Easy phylotyping of Escherichia coli via the EzClermont web app and command-line tool
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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.0.000143Abstract
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/.Funder
The James Hutton Institute; National University of Ireland, Galwayae974a485f413a2113503eed53cd6c53
https://doi.org/10.1099/acmi.0.000143
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