sistr
Tags: salmonella serotype mlst cgmlst typing sample-scope
Salmonella In Silico Typing Resource command-line tool.
This subworkflow performs comprehensive typing of Salmonella genomes using SISTR, which predicts serotype, determines subspecies, performs MLST typing, and calculates core genome MLST distances. The tool provides a one-stop solution for Salmonella classification and epidemiological typing.
Take
assembly: Channel<Record>
| Field | Description |
|---|---|
meta | Groovy Record containing sample information |
assembly | Assembly files in FASTA format for Salmonella typing |
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 | SISTR prediction results in TSV format |
allele_fasta | Novel alleles in FASTA format |
allele_json | Alleles in JSON format |
cgmlst_csv | cgMLST profile in CSV 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.
- sistr - Serovar prediction of Salmonella assemblies.
Used By
This subworkflow is used by the following workflows:
- sistr - Serovar prediction of Salmonella enterica from 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) -
SISTR
Yoshida CE, Kruczkiewicz P, Laing CR, Lingohr EJ, Gannon VPJ, Nash JHE, Taboada EN The Salmonella In Silico Typing Resource (SISTR): An Open Web-Accessible Tool for Rapidly Typing and Subtyping Draft Salmonella Genome Assemblies. PloS One, 11(1), e0147101. (2016)