shigapass

Tags: shigella eiec serotype virulence prediction sample-scope

Predict Shigella serotypes and differentiate Shigella/EIEC.

Uses ShigaPass to identify Shigella serotypes and distinguish Shigella species from Enteroinvasive Escherichia coli (EIEC) using specific genomic markers from assembled contigs.

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,
    flex_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	ShigaPass summary results in TSV format
flex_tsv	Path?	ShigaPass Flex summary 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

• shigapass - Predict serotypes of Shigella from assemblies.

Workflows

• shigapass - Prediction of Shigella serotypes and differentiation from 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)

• shigapass
  Yassine I, Hansen EE, Lefèvre S, Ruckly C, Carle I, Lejay-Collin M, Fabre L, Rafei R, Pardos de la Gandara M, Daboussi F, Shahin A, Weill FX ShigaPass: an in silico tool predicting Shigella serotypes from whole-genome sequencing assemblies. Microb Genomics 9(3) (2023)

Source

View source on GitHub

Version

SHIGAPASS:
    - shigapass: 1.5.0