shigatyper
Tags: shigella serotype typing prediction antigen-genes sample-scope
Predict serotypes of Shigella from reads or assemblies.
This subworkflow uses ShigaTyper to predict serotypes of Shigella strains from either Illumina/Nanopore reads or assembled genomes. It analyzes antigen-encoding genes to determine the serotype classification of each isolate.
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 |
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 | ShigaTyper results in TSV format |
hits | Detailed hits from ShigaTyper |
run_outputs
| Output | Description |
|---|---|
csv | Merged serotype predictions from all samples |
Module Composition
This subworkflow calls the following modules:
- shigatyper - Shigella serotype from Illumina or Oxford Nanopore reads.
- csvtk_concat - Concatenate multiple CSV or TSV files into a single table.
Used By
This subworkflow is used by the following workflows:
- shigatyper - Rapid determination of Shigella serotypes from sequencing 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) -
ShigaTyper
Wu Y, Lau HK, Lee T, Lau DK, Payne J In Silico Serotyping Based on Whole-Genome Sequencing Improves the Accuracy of Shigella Identification. Applied and Environmental Microbiology, 85(7). (2019)