clermontyping

Tags: bacteria escherichia-coli typing phylotyping pcr phylogroup sample-scope

Determine the phylogroup of Escherichia coli isolates.

Uses ClermonTyping to perform in silico PCR detection of specific marker genes (arpA, chuA, yjaA, TspE4.C2). This assigns the isolate to one of the main E. coli phylogroups (A, B1, B2, C, D, E, F, G, or Cryptic).

Inputs

record (
    meta: Record,
    fna: Path
)

Field	Type	Description
meta	Record	Groovy Record containing sample information
fna	Path	Assembled contigs in FASTA format

Outputs

record (
    meta: Record,
    tsv: Path,
    results: Set<Path>,
    logs: Set<Path?>,
    nf_logs: Set<Path>,
    versions: Set<Path>
)

Field	Type	Description
meta	Record	Sample information record
tsv	Path	Tab-delimited E. coli phylogroup assignment with detected marker genes
results	Set<Path>	All output files to be published
logs	Set<Path?>	Optional program specific log files
nf_logs	Set<Path>	Nextflow-specific log files (e.g. .command.{begin
versions	Set<Path>	A YAML formatted file with program versions

Parameters

ClermonTyping Parameters

Parameter	Type	Default	Description
--clermontyping_threshold	integer	0	Do not use contigs under this size

Used By

Subworkflows

• clermontyping - Predict phylogroups of Escherichia coli from genome assemblies.

Workflows

• clermontyping - In silico phylotyping of Escherichia genus.

Citations

If you use this in your analysis, please cite the following.

• Bactopia
  Petit III RA, Read TD Bactopia - a flexible pipeline for complete analysis of bacterial genomes. mSystems 5 (2020)

• ClermontTyping
  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, 4(7), e000192. (2018)

Source

View source on GitHub

Version

CLERMONTYPING:
    - clermontyping: 24.02