Link to bioRxiv paper:
http://biorxiv.org/cgi/content/short/2023.04.05.535718v1?rss=1
Authors: 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.
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 unbiased 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.
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