seroba
Tags: streptococcus pneumoniae serotype k-mer capsular sample-scope
k-mer based pipeline to identify the serotype of Streptococcus pneumoniae.
This subworkflow performs serotyping of Streptococcus pneumoniae from Illumina next-generation sequencing reads using Seroba. The tool uses a k-mer based approach to rapidly classify pneumococcal isolates into their respective serotypes based on the capsular polysaccharide synthesis locus.
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 |
lr | Long reads (ONT/PacBio) |
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 |
|---|---|
tsv | Serotype prediction results with predicted serotype and confidence in TSV format |
txt | Detailed information about the predicted serogroup and allele matches |
run_outputs
| Output | Description |
|---|---|
csv | Aggregated results in CSV format |
Module Composition
This subworkflow calls the following modules:
- csvtk_concat - Concatenate multiple CSV or TSV files into a single table.
- seroba_run - k-mer based Streptococcus pneumoniae serotyping.
Used By
This subworkflow is used by the following 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)