seroba_run

Tags: streptococcus-pneumoniae serotype k-mer prediction seroba sample-scope

k-mer based Streptococcus pneumoniae serotyping.

Uses SeroBA to identify the serotype of Streptococcus pneumoniae from Illumina paired-end reads using a k-mer based approach.

Database Required

Requires the SeroBA database to be set up using seroba createDBs before running.

Inputs

record (
    meta: Record,
    r1: Path,
    r2: Path
)

Field	Type	Description
meta	Record	Groovy Record containing sample information
r1	Path	Illumina R1 reads (paired-end)
r2	Path	Illumina R2 reads (paired-end)

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	Serotype prediction results with predicted serotype and confidence in TSV format
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

SeroBA Parameters

Parameter	Type	Default	Description
--seroba_coverage	integer	20	Threshold for k-mer coverage of the reference sequence

Used By

Subworkflows

• seroba - k-mer based pipeline to identify the serotype of Streptococcus pneumoniae.

Workflows

• seroba - Serotyping of Streptococcus pneumoniae from Illumina paired-end reads.

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)

• Seroba
  Epping L, van Tonder AJ, Gladstone RA, The Global Pneumococcal Sequencing Consortium, Bentley SD, Page AJ, Keane JA SeroBA: rapid high-throughput serotyping of Streptococcus pneumoniae from whole genome sequence data. Microbial Genomics, 4(7) (2018)

Source

View source on GitHub

Version

SEROBA_RUN:
    - seroba: 1.0.2