Archaea vs Bacteria

Code from paper:

Systematic genome-guided discovery of antagonistic interactions between archaea and bacteria

Romain Strock, Valerie WC Soo, Antoine Hocher, Tobias Warnecke
bioRxiv 2024.09.18.613068; doi: https://doi.org/10.1101/2024.09.18.613068

Content

• notebook/: python notebooks to reproduce all the figures.
• src/: scripts to produce all the data used in the paper. Scripts are referenced in notebooks.
• figures/: all unassembled figures as produced by the relevant notebooks.
• data/: input data and data produced by the scripts and notebooks in this repo.

Install

git clone https://github.com/srom/archaea-vs-bacteria.git
git lfs pull origin main  # optional - see below
cd archaea-vs-bacteria
conda env create -f environment.yml
conda activate AvB

Note: some of the larger files in data/ are tracked with Git Large File Storage. They won't get downloaded with git pull or through GitHub's UI. To download these files, install git-lfs and use git lfs pull.