ngmaster
Tags: neisseria-gonorrhoeae ng-mast typing gonococcal antigen sample-scope
Perform multi-antigen sequence typing of Neisseria gonorrhoeae from genome assemblies.
This subworkflow uses ngmaster to perform in silico multi-antigen sequence typing (NG-MAST) for Neisseria gonorrhoeae 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 NG-MASTER results with porB and tbpB alleles and sequence type |
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.
- ngmaster - Serotyping and Multi-Antigen Sequence Typing (MAST) of Neisseria gonorrhoeae.
Used By
This subworkflow is used by the following workflows:
- ngmaster - Multi-antigen sequence typing of Neisseria gonorrhoeae.
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) -
ngmaster
Kwong J, Gonçalves da Silva A, Schultz M, Seeman T ngmaster - In silico multi-antigen sequence typing for Neisseria gonorrhoeae (NG-MAST) (GitHub)