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.
- Python (Tested with versions 2.7 and 3.5)
- SciPy (Tested with versions 0.16, 0.17, 0.18)
If you supply custom trees (Optional)
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 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
If you use Scoary, please citing our paper
Scoary is freely available under a GPLv3 license.
Ola Brynildsrud (email@example.com)
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