• 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; The James Hutton Institute; National University of Ireland, Galway (Microbiology Society, 2020-09-01)
      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/.