Building pangenome graphs

Garrison, E; Guarracino, A; Heumos, S; Villani, F; Bao, Z; Tattini, T; Hagmann, J; Vorbrugg, S; Marco-Sola, S; Kubica, C; Ashbrook, G; Thorell, K; Rusholme-Pilcher, RL; Liti, G; Rudbeck, E; Nahnsen, S; Yang, Z; Moses, MN; Nobrega, FL; Wu, Y; Chen, H; de Ligt, J; Sudmant, PH; Soranzo, N; Colonna, V; Williams, RW; Prins, P

doi:10.1101/2023.04.05.535718

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Building pangenome graphs

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Vorbrugg, S
Department Molecular Biology, Max Planck Institute for Biology Tübingen, Max Planck Society;

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Kubica, C
Department Molecular Biology, Max Planck Institute for Biology Tübingen, Max Planck Society;

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Citation

Garrison, E., Guarracino, A., Heumos, S., Villani, F., Bao, Z., Tattini, T., et al. (submitted). Building pangenome graphs.

Cite as: https://hdl.handle.net/21.11116/0000-000C-F30F-2

Abstract

Pangenome graphs can represent all variation between multiple genomes, but existing methods for constructing them are biased due to reference-guided approaches. In response, we have developed PanGenome Graph Builder (PGGB), a reference-free pipeline for constructing unbi-ased pangenome graphs. PGGB uses all-to-all whole-genome alignments and learned graph embeddings to build and iteratively refine a model in which we can identify variation, measure conservation, detect recombination events, and infer phylogenetic relationships.