Description

Use pangenome outputs for GWAS

Input

Name (Type)
Description
Pattern

meta (map)

Groovy Map containing sample information
e.g. [ id:‘test’, single_end

]

genes (file)

A presence/absence matrix of genes in the pan-genome

*.csv

traits (file)

A CSV file containing trait information per-sample

*.csv

tree (file)

A Newick formtted tree for phylogenetic analyses

*.{dnd,nwk,treefile}

Output

Name (Type)
Description
Pattern

meta (map)

Groovy Map containing sample information
e.g. [ id:‘test’, single_end

]

versions (file)

File containing software versions

versions.yml

csv (file)

Gene associations in a CSV file per trait

*.csv

Tools

scoary
GPL v3

Microbial pan-GWAS using the output from Roary