ngmaster

Tags: bacteria neisseria-gonorrhoeae serotype typing mast porb tbpb sample-scope

Serotyping and Multi-Antigen Sequence Typing (MAST) of Neisseria gonorrhoeae.

Uses NG-MASTER to identify the alleles of the porB and tbpB genes in N. gonorrhoeae assemblies, which is the basis for the internationally recognized MAST genotyping scheme.

Inputs

record (
    meta: Record,
    fna: Path
)

Field	Type	Description
meta	Record	Groovy Record containing sample information
fna	Path	Assembled contigs in FASTA format

Outputs

record (
    meta: Record,
    tsv: Path,
    results: Set<Path>,
    logs: Set<Path?>,
    nf_logs: Set<Path>,
    versions: Set<Path>
)

Field	Type	Description
meta	Record	Sample information record
tsv	Path	Tab-delimited NG-MASTER results with porB and tbpB alleles and sequence type
results	Set<Path>	All output files to be published
logs	Set<Path?>	Optional program specific log files
nf_logs	Set<Path>	Nextflow-specific log files (e.g. .command.{begin
versions	Set<Path>	A YAML formatted file with program versions

Parameters

ngmaster Parameters

Parameter	Type	Default	Description
--ngmaster_csv	boolean	false	output comma-separated format (CSV) rather than tab-separated

Used By

Subworkflows

• ngmaster - Perform multi-antigen sequence typing of Neisseria gonorrhoeae from genome assemblies.

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)

Source

View source on GitHub

Version

NGMASTER:
    - ngmaster: 2.0.0