pneumocat
Tags: streptococcus-pneumoniae serotype capsular-typing typing sample-scope
Perform capsular typing of Streptococcus pneumoniae from NGS data.
This subworkflow uses PneumoCaT to identify serotype-specific capsular loci and determine serotypes from next-generation sequencing data. It provides comprehensive serotype determination including coverage statistics and confidence scores for each sample.
Uses explicit positional record fields for reads:
- Input: record(meta, r1, r2, se, lr) where each read slot is Path?
Take
reads: Channel<Record>
| Field | Description |
|---|---|
meta | Groovy Record containing sample information |
r1 | Illumina R1 reads (paired-end) |
r2 | Illumina R2 reads (paired-end) |
se | Single-end Illumina reads (not supported by PneumoCaT) |
lr | Long reads (not supported by PneumoCaT) |
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 |
|---|---|
xml | The PneumoCaT result files in XML format |
txt | A file containing the coverage information across the genes |
run_outputs
No run-scope outputs.
Module Composition
This subworkflow calls the following modules:
- pneumocat - Capsular typing of Streptococcus pneumoniae from Illumina reads.
Used By
This subworkflow is used by the following 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)