Building pangenome graphs

作者：Erik Garrison, Andrea Guarracino, Simon Heumos, Flavia Villani, Zhigui Bao, Lorenzo Tattini, Jörg Hagmann, Sebastian Vorbrugg, Santiago Marco‐Sola, Christian Kubica, David G. 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 · 发表于：bioRxiv (Cold Spring Harbor Laboratory) · 年份：2023 · DOI：10.1101/2023.04.05.535718 · 被引用次数：119 · 研究领域：Genomics and Phylogenetic Studies、Chromosomal and Genetic Variations、RNA and protein synthesis mechanisms

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.