scoary 1.6.11

Microbial pan-GWAS using the output from Roary

Scoary is designed to take the gene_presence_absence.csv file from Roary as well as a traits file created by the user and calculate the assocations between all genes in the accessory genome and the traits. It reports a list of genes sorted by strength of association per trait.

Dependencies

• Python (Tested with versions 2.7, 3.4, 3.5, 3.6 and 3.6-dev)

• SciPy (Tested with versions 0.16, 0.17, 0.18)

If you supply custom trees (Optional)

• ete3

• six

Note that ete3 and six are not automatically installed. You can do pip install ete3 six to get them

Using the GUI (Optional)

• Tkinter/ttk

Tkinter/ttk is already part of most python distributions. If you lack it consider getting Homebrew/Linuxbrew and running brew install python –with-tcl-tk

Installation

The easiest way to install Scoary is through the pip package manager:

pip install scoary

Usage

scoary -g <gene_presence_absence.csv> -t <traits.csv>

Documentation

The most updated documentation for scoary is found at the project site

Citation

If you use Scoary, please cite our paper

License

Scoary is freely available under a GPLv3 license.

Contact

Ola Brynildsrud ([e-mail])