Building pangenome graphs

Garrison, E.; Guarracino, A.; Heumos, S.; Villani, F.; Bao, Z.; Tattini, L.; Hagmann, J.; Vorbrugg, S.; Marco-Sola, S.; Kubica, C.; Ashbrook, D. G.; Thorell, K.; Rusholme-Pilcher, R. L.; Liti, G.; Rudbeck, E.; Nahnsen, S.; Yang, Z.; Moses, M. N.; Nobrega, F. L.; Wu, Y.; Chen, H.; de Ligt, J.; Sudmant, P. H.; Soranzo, N.; Colonna, V.; Williams, R. W.; Prins, P.

doi:10.1101/2023.04.05.535718

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bioRxiv · 10.1101/2023.04.05.535718

Building pangenome graphs

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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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Garrison, E., Guarracino, A., Heumos, S., Villani, F., Bao, Z., Tattini, L., Hagmann, J., Vorbrugg, S., Marco-Sola, S., Kubica, C., Ashbrook, D. G., Thorell, K., Rusholme-Pilcher, R. L., Liti, G., Rudbeck, E., Nahnsen, S., Yang, Z., Moses, M. N., Nobrega, F. L., Wu, Y., Chen, H., de Ligt, J., Sudmant, P. H., Soranzo, N., Colonna, V., Williams, R. W., Prins, P.. 2023-04-06. Building pangenome graphs. https://doi.org/10.1101/2023.04.05.535718

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