Parallel and fixed mutations in SARS-CoV-2 evolution

Download code and denpendency

Download the repository from GitHub. Raw data (not included in the repo due to file size and GISAID terms of use) can be acquired on request.

This project uses Bioconda to manage package dependency.

conda env update
conda activate ncov_paraFix

Run the analysis

To prepare the data for phangorn (for homoplasyFinder) and hyphy, run the following commands.

python scripts/prep_homoplasyFinder.py
python scripts/prep_hyphy.py

To run the analysis, use the following commands.

Rscript scripts/run_homoplasyFinder.R # homoplasy
bash scripts/run_hyphy_meme.sh # episodic positive selection
bash scripts/run_hyphy_fubar.sh # pervasive  positive selection
Rscript scripts/run_sitePath.R # paraFix sites

To prepare for plotting the spatial-temporal distribution of mutated sites, run the following.

python scripts/prep_mutation_num.py

Visualize the result

Launch the jupyter notebook from the root directory of the project

jupyter-notebook

Open parse_hyphy.ipynb and run the notebook to parse the output of hyphy.

Open plot_result_comparison.ipynb and run the notebook to visualize the comparison between paraFix and episodic positive selection sites.

Open plot_mutation_num.ipynb and run the notebook to visualize the spatial-temporal distribution of mutated sites