Building pangenome graphs
journal contribution
posted on 2025-03-05, 04:46 authored by Erik Garrison, Andrea Guarracino, Simon Heumos, Flavia Villani, Zhigui Bao, Lorenzo Tattini, Jörg Hagmann, Sebastian Vorbrugg, Santiago Marco-Sola, Christian Kubica, Ashbrook, David G., Kaisa Thorell, Rachel L. Rusholme-Pilcher, Gianni Liti, Emilio Rudbeck, Agnieszka A. Golicz, Sven Nahnsen, Zuyu Yang, Moses Njagi Mwaniki, Franklin L. Nobrega, Yi Wu, Hao Chen, Joep de Ligt, Peter H. Sudmant, Sanwen Huang, Detlef Weigel, Nicole Soranzo, Vincenza Colonna, Robert W. Williams, Pjotr PrinsPangenome 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, a pipeline for constructing pangenome graphs without bias or exclusion. The PanGenome Graph Builder 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.