pggb: the PanGenome Graph Builder

PGGB builds pangenome variation graphs from a set of input sequences.

A pangenome variation graph can be understood as a kind of multiple sequence alignment. It lets us understand any kind of sequence variation between a collection of genomes. It shows us similarity where genomes walk through the same parts of the graph, and differences where they do not.

PGGB generates this kind of graph using an all-to-all alignment of input sequences (wfmash), graph induction (seqwish), and progressive normalization (smoothxg, gfaffix). After construction, PGGB generates diagnostic visualizations of the graph (odgi). A variant call report (in VCF) representing both small and large variants may be generated based on any reference genome included in the graph (vg). PGGB writes its output in GFAv1 format, which can be used as input by numerous "genome graph" and pangenome tools, such as the VG and ODGI toolkits.

PGGB has been tested at scale in the Human Pangenome Reference Consortium (HPRC) as a method to build a graph from the draft human pangenome.