This repository contains custom scripts and pipelines to analyse Chinese indicine cattle project. Most of the scripts were specially designed to perform the analyses in the paper A Chinese indicine pan-genome reveals a wealth of novel structural variants introgressed from other Bos species.
The analysis pipelines and scripts of the five parts of the article are integrated into the following five folders, and each script has detailed code comments.
Here is a brief description of the contents of each directory.
In addition, we provided a testing protocol for pangenome graphs.