Building pangenome graphs
Open accessPublished version of a preprint
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, 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.
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Cited by
Sorted by citations
A draft human pangenome reference.
Liao, W.-W., Asri, M., Ebler, J., Doerr, D., Haukness, M., Hickey, G., Lu, S., Lucas, J. K., Monlong, J., Abel, H. J., et al. (2023) · Nature · doi:10.1038/s41586-023-05896-x · Cited by 1,129 · see citing works
Self-citationRecombination between heterologous human acrocentric chromosomes
Guarracino, A., Buonaiuto, S., de Lima, L. G., Potapova, T., Rhie, A., Koren, S., Rubinstein, B., Fischer, C., Human Pangenome Reference Consortium, Abel, H. J., et al. (2023) · Nature · doi:10.1038/s41586-023-05976-y · Cited by 134 · see citing works
Self-citationGaps and complex structurally variant loci in phased genome assemblies
Porubsky, D., Vollger, M. R., Harvey, W. T., Rozanski, A. N., Ebert, P., Hickey, G., Hasenfeld, P., Sanders, A. D., Stober, C., Human Pangenome Reference Consortium, et al. (2023) · Genome Research · doi:10.1101/gr.277334.122 · Cited by 58 · see citing works
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- 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., Golicz, A. A., Nahnsen, S., Yang, Z., Mwaniki, M. N., Nobrega, F. L., Wu, Y., Chen, H., de Ligt, J., Sudmant, P. H., Huang, S., Weigel, D., Soranzo, N., Colonna, V., Williams, R. W., & Prins, P.
- Affiliations
- University of Tennessee Health Science Center (US)
- Universitätsklinikum Tübingen (DE)
- Agricultural Genomics Institute at Shenzhen (CN)
- Centre National de la Recherche Scientifique (FR)
- Max Planck Institute for Biology (DE)
- University of Gothenburg (SE)
- Justus-Liebig-Universität Gießen (DE)
- New Zealand Institute for Public Health and Forensic Science (NZ)
- University of Pisa (IT)
- University of Southampton (GB)
- University of California, Berkeley (US)
- University of Cambridge (GB)
- Corresponding author
- Garrison, Erik
- ORCID
- Garrison, Erik
- Guarracino, Andrea
- Heumos, Simon
- Villani, Flavia
- Bao, Zhigui
- Tattini, Lorenzo
- Hagmann, Jörg
- Vorbrugg, Sebastian
- Marco-Sola, Santiago
- Kubica, Christian
- Ashbrook, David G.
- Thorell, Kaisa
- Rusholme-Pilcher, Rachel L.
- Liti, Gianni
- Golicz, Agnieszka A.
- Nahnsen, Sven
- Yang, Zuyu
- Mwaniki, Moses Njagi
- Nobrega, Franklin L.
- Wu, Yi
- Chen, Hao
- de Ligt, Joep
- Sudmant, Peter H.
- Huang, Sanwen
- Weigel, Detlef
- Soranzo, Nicole
- Colonna, Vincenza
- Williams, Robert W.
- Prins, Pjotr
- Venue
- Nature Methods
- Published
- 2024-10-21
- Volume
- 21
- Issue
- 11
- Pages
- 2008-2012
- ISSN
- 1548-7091 (ISSN-L)
- 1548-7105
- PMC
- PMC10104075
- OpenAlex
- W4403609447
- Cited by
- 277
- References
- 8
- Citations by year
- 2026: 107 · 2025: 95 · 2024: 56 · 2023: 19
- FWCI
- 33.57
- Type
- journal article
- Language
- en
- Open access
- green
- doi.org
- Licence
- Locations
- Nature Methods (publishedVersion)
- bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion, cc-by)
- PubMed (publishedVersion)
- UPCommons institutional repository (Universitat Politècnica de Catalunya) (submittedVersion, cc-by-nc-nd)
- PubMed Central (submittedVersion, cc-by)
- Figshare (submittedVersion)
- Funders
- National Science Foundation (2118709)
- U.S. Department of Health and Human Services (U01DA047638, R01GM123489)
- Alexander von Humboldt-Stiftung
- European Commission (956229)
- Deutsche Forschungsgemeinschaft
- Bundesministerium für Bildung und Forschung (031A537C, 031A533A, 031A532B, 031A533A, 031A533B, 031A534A, 031A535A, 031A537A, 031A537B, 031A537C, 031A537D, 031A538A, 031A535A, 031A537A, 031A538A, 031A537D, 031A534A, 031A532B, 031A533B, 031A537B)
- Nederlandse Organisatie voor Wetenschappelijk Onderzoek (2021.040)
- Max-Planck-Gesellschaft
- Bundesministerium für Wirtschaft und Energie
- German Network for Bioinformatics Infrastructure (031A533A, 031A534A, 031A538A, 031A537 A, 031A537D, 031 A535 A, 031 A537B, 031 A532B, 031 A533B, #031A537C, 031A532B,031A533A,031A533B,031A534A,031A535A,031A537A,031A537B,031A537C,031A537D,031A538A)
- National Institutes of Health
- High Performance Research Computing, Texas A and M University
- Biotechnology and Biological Sciences Research Council (BBS/E/ER/230003C, BBS/E/ER/230003A, BBS/E/ER/230002A, BBS/E/ER/230002B)
- National Institute on Drug Abuse (NIDA U01DA047638, U01DA047638)
- National Human Genome Research Institute (R01HG013017)
- National Institute of General Medical Sciences (R01GM123489, R35GM142916)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genome Rearrangement Algorithms
- Physical Sciences › Computer Science › Artificial Intelligence › Algorithms and Data Compression
- Keywords
- pangenome graphs, variation graphs, recombination detection, phylogenetic inference, genomic variation, complex sequences
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