bgwas3

A pipeline for the pangenome-wide assocation testing of multiple bacteria phenotypes.

Install

conda install -c g-r-eg bgwas3

Quick Usage

1. Create and cd into an empty project directory
2. Put all fastqs into a sub-directory named "fastqs"
3. Put reference genome (.fa) and annotations (.gff) into a directory named "refs"
4. Create a tsv file named 'phenos.tsv' with an 'id' column and one or more 'pheno_xxx' columns
5. Run:

bgwas3 make full

6. View results with:

open results/plots/index.html

More documentation coming soon.