meningotype
Tags: neisseria-meningitidis serotype finetype bexsero meningococcal sample-scope
Predict serotypes of Neisseria meningitidis from genome assemblies.
This subworkflow uses meningotype to perform in silico serotyping, finetyping and Bexsero antigen sequence typing of Neisseria meningitidis strains from assembled genomes. 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 | Tab-delimited meningotype results with serogroup, PorA, and FetA predictions |
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.
- meningotype - Serotyping and finetyping of Neisseria meningitidis.
Used By
This subworkflow is used by the following workflows:
- meningotype - Comprehensive typing of Neisseria meningitidis.
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) -
meningotype
Kwong JC, Gonçalves da Silva A, Stinear TP, Howden BP, & Seemann T meningotype: in silico typing for Neisseria meningitidis. (GitHub)