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

1. Download the 'reads' subfolder, 'ref' subfolder, and two Jupyter notebook files.
2. Configure a working directory with the necessary data analysis tools by running the commands in the 'configure-working-directory.ipynb' Jupyter Notebook
3. 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.