meningotype

Tags: bacteria neisseria-meningitidis serotype serogroup finetyping pora feta capsule sample-scope

Serotyping and finetyping of Neisseria meningitidis.

Uses Meningotype to predict the serogroup (capsule), PorA variable regions, and FetA variable regions of N. meningitidis assemblies. This provides a comprehensive molecular typing profile (e.g., B:P1.7-2,4:F1-5) used in surveillance.

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 meningotype results with serogroup, PorA, and FetA predictions
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

meningotype Parameters

You can use these parameters to fine-tune your meningotype analysis

Parameter	Type	Default	Description
--meningotype_finetype	boolean	false	perform porA and fetA fine typing
--meningotype_porB	boolean	false	perform porB sequence typing (NEIS2020)
--meningotype_bast	boolean	false	perform Bexsero antigen sequence typing (BAST)
--meningotype_mlst	boolean	false	perform MLST
--meningotype_all	boolean	false	perform MLST, porA, fetA, porB, BAST typing

Used By

Subworkflows

• meningotype - Predict serotypes of Neisseria meningitidis from genome assemblies.

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)

Source

View source on GitHub

Version

MENINGOTYPE:
    - meningotype: 0.8.6b