Chinese indicine cattle pan-genome project

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.

Contents

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.

• assembly and assessment

• multi-assembly graph construction

• structural variants generating and characterizing

• archaic introgression and_admixture history analysis

• structural variants genotyping and adaptive introgression analysis

Here is a brief description of the contents of each directory.

In addition, we provided a testing protocol for pangenome graphs.