ssuissero

Tags: streptococcus-suis serotype typing prediction sample-scope

Serotype prediction of Streptococcus suis assemblies.

Uses SsuisSero to predict the serotype of Streptococcus suis strains from genome assemblies based on the presence of specific capsular genes.

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	SsuisSero 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

• ssuissero - Predict serotypes of Streptococcus suis from genome assemblies.

Workflows

• ssuissero - Serotype prediction of Streptococcus suis assemblies.

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)

• SsuisSero
  Lui J SsuisSero: Rapid Streptococcus suis serotyping (GitHub)

Source

View source on GitHub

Version

SSUISSERO:
    - ssuissero: 1.0.1