hpsuissero
Tags: haemophilus parasuis serotype epidemiology sample-scope
Rapid Haemophilus parasuis serotyping.
This subworkflow performs serotyping of Haemophilus parasuis using HpsuisSero, which identifies serotype-specific markers in genome assemblies. The tool provides rapid classification of H. parasuis isolates into their respective serotypes, which is important for epidemiological surveillance and vaccine development.
Take
assembly: Channel<Record>
| Field | Description |
|---|---|
meta | Groovy Record containing sample information |
assembly | Assembly files in FASTA format for H. parasuis serotype prediction |
Emit
Published
The sample_outputs and run_outputs emissions are aggregates of output files that will be published in the entry workflow.
sample_outputs
| Output | Description |
|---|---|
tsv | Tab-delimited HpsuisSero serotype prediction results |
run_outputs
| Output | Description |
|---|---|
csv | Aggregated results in CSV format |
Module Composition
This subworkflow calls the following modules:
- csvtk_concat - Concatenate multiple CSV or TSV files into a single table.
- hpsuissero - Predict Haemophilus parasuis serotype.
Used By
This subworkflow is used by the following 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)