Building pangenome graphs

Erik P. Garrison; Andrea Guarracino; Simon Heumos; Flavia Villani; Zhigui Bao; Lorenzo Tattini; Jörg Hagmann; Sebastian Vorbrugg; Santiago Marco‐Sola; Christian Kubica; David George Ashbrook; Kaisa Thorell; Rachel Rusholme‐Pilcher; Gianni Liti; Emilio Rudbeck; Agnieszka A. Golicz; Sven Nahnsen; Zuyu Yang; Moses Njagi Mwaniki; Franklin L. Nóbrega; Yi Wu; Hao Chen; Joep de Ligt; Peter H. Sudmant; Sanwen Huang; Detlef Weigel; Nicole Soranzo; Vincenza Colonna; Robert W. Williams; Pjotr Prins

doi:10.1038/s41592-024-02430-3

BioinformaticsNature MethodsOct 21, 2024

Peer-reviewed journal article

Building pangenome graphs

Erik P. Garrison iD, Andrea Guarracino iD, Simon Heumos iD, Flavia Villani iD, Zhigui Bao iD, Lorenzo Tattini iD, Jörg Hagmann iD, Sebastian Vorbrugg iD, Santiago Marco‐Sola iD, Christian Kubica iD, David George Ashbrook iD, Kaisa Thorell iD, Rachel Rusholme‐Pilcher iD, Gianni Liti iD, Emilio Rudbeck, Agnieszka A. Golicz iD, Sven Nahnsen iD, Zuyu Yang iD, Moses Njagi Mwaniki iD, Franklin L. Nóbrega iD, Yi Wu iD, Hao Chen iD, Joep de Ligt iD, Peter H. Sudmant iD, Sanwen Huang iD, , Pjotr Prins iD

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.

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