Author/Authors :
Waters, Nicholas R. Department of Microbiology - School of Natural Sciences - National University of Ireland, Galway, Ireland , Abram, Florence Department of Microbiology - School of Natural Sciences - National University of Ireland, Galway, Ireland , Brennan, Fiona Department of Microbiology - School of Natural Sciences - National University of Ireland, Galway, Ireland , Holmes, Ashleigh Cell and Molecular Sciences - James Hutton Institute, Invergowrie, Dundee DD2 5DA, Scotland , Pritchard, Leighton Information and Computational Sciences - James Hutton Institute, Invergowrie, Dundee DD2 5DA, Scotland
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 :
phylogroups web app , classification , bioinformatics , genomics; Escherichia coli
