Building pangenome graphs

Abstract
Pangenome graphs can represent all variation between multiple reference genomes, but current approaches to build them exclude complex sequences or are based upon a single reference. In response, we developed the PanGenome Graph Builder (PGGB), a pipeline for constructing pangenome graphs without bias or exclusion. PGGB uses all-to-all alignments to build a variation graph in which we can identify variation, measure conservation, detect recombination events, and infer phylogenetic relationships.
Competing Interest Statement
Author J.H. is employed by Computomics GmbH.
Footnotes
This version of the manuscript has been revised to include experimental evidence backing up our claims that using the entire pangenome without filtering is important. These results are presented as supplementary data inline in this manuscript.
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