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 language | English |
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Article number | 000143 |
Number of pages | 5 |
Journal | Access Microbiology |
Volume | 2 |
Issue number | 9 |
DOIs | |
Publication status | Published - 19 Jun 2020 |
Keywords
- ECOR, Escherichia coli Reference Collection
- MLST, multilocus sequence typing