ectyper
Tags: escherichia coli serotype o-antigen h-antigen sample-scope
In silico prediction of Escherichia coli serotype.
This subworkflow performs serotype prediction for Escherichia coli genomes using ECTyper, which predicts O and H antigens from whole genome assemblies. The tool identifies specific serotype markers and provides comprehensive serotype classification.
Take
assembly: Channel<Record>
| Field | Description |
|---|---|
meta | Groovy Record containing sample information |
assembly | Assembly files in FASTA format for E. coli serotype prediction |
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 | Tab-delimited ECTyper serotype prediction results |
txt | ECTyper detailed results in text format |
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.
- ectyper - Predict Escherichia coli serotype (O and H antigens).
Used By
This subworkflow is used by the following workflows:
- ectyper - In silico prediction of Escherichia coli serotype.
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) -
ECTyper
Laing C, Bessonov K, Sung S, La Rose C ECTyper - In silico prediction of Escherichia coli serotype (GitHub)