Scoary - Microbial pan-GWAS ###########################
Scoary <https://github.com/AdmiralenOla/Scoary>_ is designed to take the gene_presence_absence.csv file from Roary <https://sanger-pathogens.github.io/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.
- Python (Tested with versions 2.7, 3.4, 3.5, 3.6 and 3.6-dev)
SciPy <http://www.scipy.org/install.html>_ (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
The easiest way to install Scoary is through the pip package manager::
pip install scoary
scoary -g <gene_presence_absence.csv> -t <traits.csv>
The most updated documentation for scoary is found at the project site <https://github.com/AdmiralenOla/Scoary>_
If you use Scoary, please cite our paper <https://dx.doi.org/10.1186/s13059-016-1108-8>_
Scoary is freely available under a GPLv3 license.
Ola Brynildsrud (ola.brynildsrud@fhi.no)