gigatyper
Tags: mlst typing multi-scheme sample-scope
Run all available MLST schemes for a species against an assembly
This subworkflow uses GigaTyper to run all available mlst schemes for a species against an assembly. 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 | MLST results across all schemes |
run_outputs
| Output | Description |
|---|---|
csv | A merged TSV file with gigatyper results from all samples |
Module Composition
This subworkflow calls the following modules:
- csvtk_concat - Concatenate multiple CSV or TSV files into a single table.
- gigatyper - Run all available MLST schemes for a species against an assembly
Used By
This subworkflow is used by the following workflows:
- gigatyper - Run all available MLST schemes for a species against an assembly
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) -
GigaTyper
Petit III RA, Fearing T, Groves E GigaTyper: Why choose one scheme when you can flex them all? (GitHub)