shigapass
Tags: shigella serotype typing prediction antigen-genes sample-scope
Predict serotypes of Shigella from assemblies.
This subworkflow uses ShigaPass to predict serotypes of Shigella strains from assembled genomes. It analyzes the presence and composition of antigen-encoding genes to classify isolates into their known serotypes.
Take
assembly: Channel<Record>
| Field | Description |
|---|---|
meta | Groovy Record containing sample information |
assembly | Assembled contigs in FASTA format |
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 | ShigaPass summary results in TSV format |
flex_tsv | ShigaPass Flex summary results in TSV format |
run_outputs
| Output | Description |
|---|---|
csv | Aggregated results in CSV format |
Module Composition
This subworkflow calls the following modules:
- shigapass - Predict Shigella serotypes and differentiate Shigella/EIEC.
- csvtk_concat - Concatenate multiple CSV or TSV files into a single table.
Used By
This subworkflow is used by the following workflows:
- shigapass - Prediction of Shigella serotypes and differentiation from EIEC.
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) -
shigapass
Yassine I, Hansen EE, Lefèvre S, Ruckly C, Carle I, Lejay-Collin M, Fabre L, Rafei R, Pardos de la Gandara M, Daboussi F, Shahin A, Weill FX ShigaPass: an in silico tool predicting Shigella serotypes from whole-genome sequencing assemblies. Microb Genomics 9(3) (2023)