Introduction
This folder contains files and data from the manuscript 'Non-pathogenic infection of macaques and baboons with a baboon arterivirus.'
Reproducing read mapping and variant calls
- Download the 'reads' subfolder, 'ref' subfolder, and two Jupyter notebook files.
- Configure a working directory with the necessary data analysis tools by running the commands in the 'configure-working-directory.ipynb' Jupyter Notebook
- Running the commands in the 'SWBV-baboon-macaque-challenge.ipynb' Jupyter Notebook will regenerate the exact read mappings and variant calls used in the manuscript
Inspecting pre-calculated read mapping and variant calls
The results in the 'map to reference' folder contain the mapping and variant call results that are generated by running the 'SWBV-baboon-macaque-challenge.ipynb' Jupyter Notebook.