lissero
Tags: listeria monocytogenes serotype outbreak sample-scope
In silico serotype prediction for Listeria monocytogenes.
This subworkflow performs serotype prediction for Listeria monocytogenes using LisSero, which identifies specific serotype markers in genome assemblies. The tool provides rapid classification into the major L. monocytogenes serotypes, which is important for outbreak investigation and tracking.
Take
assembly: Channel<Record>
| Field | Description |
|---|---|
meta | Groovy Record containing sample information |
assembly | Assembly files in FASTA format for L. monocytogenes 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 LisSero results with predicted serogroup and marker gene detection |
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.
- lissero - Predict Listeria monocytogenes serogroup.
Used By
This subworkflow is used by the following workflows:
- lissero - Serogroup typing prediction for Listeria monocytogenes.
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) -
LisSero
Kwong J, Zhang J, Seeman T, Horan, K, Gonçalves da Silva A LisSero - In silico serotype prediction for Listeria monocytogenes (GitHub)