scoary
Tags: gwas association pan-genome traits statistical run-scope
Pan-genome wide association studies.
This subworkflow performs genome-wide association studies (GWAS) on pan-genome data using Scoary. The tool identifies genes associated with binary traits such as pathogenicity, host specificity, or antibiotic resistance. It calculates statistical associations between gene presence/absence and phenotypic traits across multiple bacterial isolates.
Take
csv: Channel<Record>
| Field | Description |
|---|---|
meta | Groovy Record containing sample information |
csv | Gene presence/absence matrix from pan-genome analysis in CSV format |
traits: Path?
| Name | Type | Description |
|---|---|---|
traits | Path? | Trait file containing binary phenotypic characteristics for each isolate (optional) |
Emit
Published
The sample_outputs and run_outputs emissions are aggregates of output files that will be published in the entry workflow.
sample_outputs
No sample-scope outputs.
run_outputs
No run-scope outputs.
Module Composition
This subworkflow calls the following modules:
- scoary - Pan-genome wide association studies.
Used By
This subworkflow is used by the following workflows:
- pangenome - Pangenome analysis with optional core-genome phylogeny.
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) -
Scoary
Brynildsrud O, Bohlin J, Scheffer L, Eldholm V Rapid scoring of genes in microbial pan-genome-wide association studies with Scoary. Genome Biol. 17:238 (2016)