ssuissero

Tags: streptococcus-suis serotype typing prediction capsular-genes sample-scope

Predict serotypes of Streptococcus suis from genome assemblies.

This subworkflow uses SsuisSero to predict serotypes of Streptococcus suis strains from genome assemblies based on the presence of specific capsular genes. It processes each sample individually and aggregates the results into a single consolidated report.

Take

assembly: Channel<Record>

Field	Description
meta	Groovy Record containing sample information
assembly	Assembled contigs in FASTA format

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	SsuisSero results in TSV format

run_outputs

Output	Description
csv	Aggregated results in CSV format

Module Composition

This subworkflow calls the following modules:

• ssuissero - Serotype prediction of Streptococcus suis assemblies.
• csvtk_concat - Concatenate multiple CSV or TSV files into a single table.

Used By

This subworkflow is used by the following 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