Building pangenome graphs

To understand the sequence relationships between many genomes, we build a graphical data structure that represents their mutual alignment. This pangenome graph can serve as a powerful tool for research into genome variation, selection, and evolution. Generating and refining pangenome graphs is an area of active research that has necessitated the development of novel alignment and graph induction methods. We discuss these issues in detail and illustrate how they are addressed in the pangenome graph builder tool (pggb). We close with an overview of the application of our approach to the 90 haplotypes in the year 1 assemblies of the Human Pangenome Project, where our method provides an unprecedented view of variation in the full human pangenome.