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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 contigs into a sub-directory named "contigs"

3. Create a tsv file with an 'id' column and one or more 'pheno_xxx' columns

4. Run:

::

bgwas3 make full

5. View results with:

::

open results/plots/index.html

More documentation coming soon.