stxtyper
Tags: stx shiga-toxin typing stec virulence sample-scope
Identify and type Stx operons from assembled genomic sequences
This subworkflow uses StxTyper to identify and type stx operons from assembled genomic sequences. It processes each sample individually and aggregates the results into a single consolidated report.
Take
fna: Channel<Record>
| Field | Description |
|---|---|
meta | Groovy Record containing sample information |
fna | 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 | Tab-delimited Stx operon typing results |
run_outputs
| Output | Description |
|---|---|
csv | A merged TSV file with stxtyper results from all samples |
Module Composition
This subworkflow calls the following modules:
- csvtk_concat - Concatenate multiple CSV or TSV files into a single table.
- stxtyper - Identify and type Stx operons from assembled genomic sequences
Used By
This subworkflow is used by the following workflows:
- stxtyper - Identify and type Stx operons from assembled genomic sequences
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) -
StxTyper
Feldgarden M, Brover V, Gonzalez-Escalona N, Frrat JG, Haendiges J, Haft DH, Hoffmann M, Pettengill JB, Prasad AB, Tillman GE, Tyson GH, Klimke W AMRFinderPlus and the Reference Gene Catalog facilitate examination of the genomic links among antimicrobial resistance, stress response, and virulence. Scientific Reports 11, 12728 (2021)