shigeifinder

Tags: shigella eiec serotype identification cluster virulence sample-scope

Shigella and EIEC serotyping from assemblies.

Uses ShigEiFinder to differentiate Shigella and Enteroinvasive E. coli (EIEC) and predict their serotypes from genome assemblies. It utilizes cluster-specific marker genes to distinguish these closely related pathovars.

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	ShigEiFinder results in TSV format
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

Used By

Subworkflows

• shigeifinder - Predict serotypes of Shigella and EIEC from assemblies.

Workflows

• shigeifinder - In silico serotype prediction for Shigella and Enteroinvasive E. coli (EIEC).

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)

• ShigEiFinder
  Zhang X, Payne M, Nguyen T, Kaur S, Lan R Cluster-specific gene markers enhance Shigella and enteroinvasive Escherichia coli in silico serotyping. Microbial Genomics, 7(12). (2021)

Source

View source on GitHub

Version

SHIGEIFINDER:
    - shigeifinder: 1.3.5