shigeifinder
Tags: shigella eiec serotype typing cluster-analysis sample-scope
Predict serotypes of Shigella and EIEC from assemblies.
This subworkflow uses ShigEiFinder to predict serotypes of Shigella and Enteroinvasive E. coli (EIEC) from assembled genomes. It uses a cluster-informed approach to identify specific serotype markers and classify isolates based on their antigenic profiles.
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 | ShigEiFinder results in TSV format |
run_outputs
| Output | Description |
|---|---|
csv | Aggregated results in CSV format |
Module Composition
This subworkflow calls the following modules:
- shigeifinder - Shigella and EIEC serotyping from assemblies.
- csvtk_concat - Concatenate multiple CSV or TSV files into a single table.
Used By
This subworkflow is used by the following workflows:
- shigeifinder - In silico serotype prediction for Shigella and Enteroinvasive E. coli (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) -
ShigEiFinder
Zhang X, Payne M, Nguyen T, Kaur S, Lan R Cluster-specific gene markers enhance Shigella and enteroinvasive Escherichia coli in silico serotyping. Microbial Genomics, 7(12). (2021)