ClermonTypingClermonTyping is an in silico PCR-based method for phylogroup determination of Escherichia coli genome assemblies. It detects specific genetic markers using BLAST to assign E. coli strains to Clermont phylogroups (A, B1, B2, C, D, E, F, and cryptic clades).Versions

v24.02 (default)

Tags: Escherichia coli, phylogroup typing, in silico PCRParameters

fasta_files (file, multiple) required: Input FASTA genome assemblies of Escherichia coli.

threshold (int): Remove contigs below this size (bp) before typing. Set to 0 to disable filtering.

Links

License: GPL-3.0

Cite as: Beghain J, Bridier-Nahmias A, Le Nagard H, Denamur E, Clermont O. Clermontyping: an easy-to-use and accurate in silico method for Escherichia genus strain phylotyping. Microbial Genomics (2018). doi:10.1099/mgen.0.000192

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