seqsero2
Tags: salmonella serotype prediction foodborne enteric sample-scope
Predict Salmonella serotypes from genome assemblies.
This subworkflow uses SeqSero2 to predict the serotypes of Salmonella strains from assembled genomes. It processes each sample individually and aggregates the results into a single consolidated report.
Take
seqs: 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 | SeqSero2 serotype prediction results in TSV format |
txt | SeqSero2 serotype prediction 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.
- seqsero2 - Salmonella serotype prediction from genome sequencing data.
Used By
This subworkflow is used by the following workflows:
- seqsero2 - Salmonella serotype prediction from sequencing reads or assemblies.
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) -
SeqSero2
Zhang S, Den-Bakker HC, Li S, Dinsmore BA, Lane C, Lauer AC, Fields PI, Deng X. SeqSero2: rapid and improved Salmonella serotype determination using whole genome sequencing data. Appl Environ Microbiology 85(23):e01746-19 (2019)