hpsuissero

Tags: bacteria haemophilus-parasuis glaesserella-parasuis serotype typing capsule sample-scope

Predict Haemophilus parasuis serotype.

Uses HPSuisSero to predict the serotype of Haemophilus parasuis (syn. Glaesserella parasuis) assemblies. It detects specific capsule loci markers to assign one of the known serovars.

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 Haemophilus parasuis serotype prediction results
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

• hpsuissero - Rapid Haemophilus parasuis serotyping.

Workflows

• hpsuissero - Serotype prediction of Haemophilus parasuis 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)

• HpsuisSero
  Lui J HpsuisSero: Rapid Haemophilus parasuis serotyping (GitHub)

Source

View source on GitHub

Version

HPSUISSERO:
    - hpsuissero: 1.0.1