pneumocat

Tags: pneumocat streptococcus-pneumoniae capsular-typing serotyping sample-scope

Capsular typing of Streptococcus pneumoniae from Illumina reads.

Uses PneumoCaT (Pneumococcal Capsular Typing) to assign capsular types to Streptococcus pneumoniae using a two-step approach: first matching reads to a global database, then using a mapped-based approach for specific serogroup differentiation.

Uses explicit positional record fields for reads:

• Input: record(meta, r1, r2) where each read slot is Path

Negative results will cause non-0 exit codes from PneumoCaT

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,
    xml: Path?,
    txt: Path?,
    results: Set<Path>,
    logs: Set<Path?>,
    nf_logs: Set<Path>,
    versions: Set<Path>
)

Field	Type	Description
meta	Record	Sample information record
xml	Path?	The PneumoCaT result files in XML format
txt	Path?	A file containing the coverage information across the genes
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

Used By

Subworkflows

• pneumocat - Perform capsular typing of Streptococcus pneumoniae from NGS data.

Workflows

• pneumocat - Capsular type assignment to Streptococcus pneumoniae from sequence 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)

• PneumoCaT
  Kapatai G, Sheppard CL, Al-Shahib A, Litt DJ, Underwood AP, Harrison TG, and Fry NK Whole genome sequencing of Streptococcus pneumoniae: development, evaluation and verification of targets for serogroup and serotype prediction using an automated pipeline. PeerJ, 4, e2477. (2016)

• Bowtie2
  Langmead B, Salzberg SL Fast gapped-read alignment with Bowtie 2. Nat. Methods. 9, 357-359 (2012)

Source

View source on GitHub

Version

PNEUMOCAT:
    - pneumocat: 1.2.1