stecfinder
Tags: escherichia-coli stec serotype virulence-genes shiga-toxin sample-scope
Identify and serotype Shiga toxin-producing E. coli (STEC) from assemblies.
This subworkflow uses STECFinder to identify and serotype Shiga toxin-producing E. coli (STEC) strains using genomic cluster-specific markers. It screens assemblies for virulence genes and serotype markers to classify STEC isolates into their known serotypes.
Take
seqs: Channel<Record>
| Field | Description |
|---|---|
meta | Groovy Record containing sample information |
fna | Assembled contigs in FASTA format |
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 | TSV file with STEC gene markers results |
run_outputs
| Output | Description |
|---|---|
csv | Merged STEC results from all samples |
Module Composition
This subworkflow calls the following modules:
- stecfinder - Serotype of Shigatoxin producing E. coli using reads/assemblies.
- csvtk_concat - Concatenate multiple CSV or TSV files into a single table.
Used By
This subworkflow is used by the following workflows:
- stecfinder - Serotype identification of Shiga toxin-producing E. coli.
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) -
STECFinder
Zhang X, Payne M, Kaur S, and Lan R Improved Genomic Identification, Clustering, and Serotyping of Shiga Toxin-Producing Escherichia coli Using Cluster/Serotype-Specific Gene Markers. Frontiers in Cellular and Infection Microbiology, 11, 772574. (2021)