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Building pangenome graphs

Building pangenome graphs
Building pangenome graphs

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.

1548-7091
2008-2012
Garrison, Erik
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Guarracino, Andrea
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Heumos, Simon
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Villani, Flavia
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Bao, Zhigui
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Tattini, Lorenzo
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Hagmann, Jörg
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Vorbrugg, Sebastian
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Marco-Sola, Santiago
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Kubica, Christian
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Ashbrook, David g.
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Thorell, Kaisa
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Rusholme-Pilcher, Rachel l.
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Liti, Gianni
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Rudbeck, Emilio
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Golicz, Agnieszka a.
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Nahnsen, Sven
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Yang, Zuyu
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Mwaniki, Moses njagi
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Nobrega, Franklin l.
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Wu, Yi
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Chen, Hao
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De ligt, Joep
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Sudmant, Peter h.
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Huang, Sanwen
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Weigel, Detlef
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Soranzo, Nicole
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Colonna, Vincenza
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Williams, Robert w.
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Prins, Pjotr
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Garrison, Erik
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Guarracino, Andrea
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Heumos, Simon
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Villani, Flavia
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Bao, Zhigui
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Tattini, Lorenzo
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Hagmann, Jörg
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Vorbrugg, Sebastian
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Marco-Sola, Santiago
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Kubica, Christian
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Ashbrook, David g.
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Thorell, Kaisa
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Rusholme-Pilcher, Rachel l.
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Liti, Gianni
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Rudbeck, Emilio
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Golicz, Agnieszka a.
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Nahnsen, Sven
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Yang, Zuyu
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Mwaniki, Moses njagi
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Nobrega, Franklin l.
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Wu, Yi
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Chen, Hao
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De ligt, Joep
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Sudmant, Peter h.
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Huang, Sanwen
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Weigel, Detlef
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Soranzo, Nicole
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Colonna, Vincenza
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Williams, Robert w.
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Prins, Pjotr
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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, Rudbeck, Emilio, 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. and Prins, Pjotr (2024) Building pangenome graphs. Nature Methods, 21 (11), 2008-2012. (doi:10.1038/s41592-024-02430-3).

Record type: Article

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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More information

Submitted date: 26 August 2024
e-pub ahead of print date: 21 October 2024
Published date: 21 October 2024
Learn more about the Institute for Life Sciences Learn more about the School of Biological Sciences

Identifiers

Local EPrints ID: 510593
URI: http://eprints.soton.ac.uk/id/eprint/510593
DOI: doi:10.1038/s41592-024-02430-3
ISSN: 1548-7091
PURE UUID: 1d48a31f-4ed3-46d5-b391-df03c2ef07dc
ORCID for Franklin l. Nobrega: ORCID iD orcid.org/0000-0002-8238-1083

Catalogue record

Date deposited: 14 Apr 2026 16:31
Last modified: 15 Apr 2026 02:01

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Contributors

Author: Erik Garrison
Author: Andrea Guarracino
Author: Simon Heumos
Author: Flavia Villani
Author: Zhigui Bao
Author: Lorenzo Tattini
Author: Jörg Hagmann
Author: Sebastian Vorbrugg
Author: Santiago Marco-Sola
Author: Christian Kubica
Author: David g. Ashbrook
Author: Kaisa Thorell
Author: Rachel l. Rusholme-Pilcher
Author: Gianni Liti
Author: Emilio Rudbeck
Author: Agnieszka a. Golicz
Author: Sven Nahnsen
Author: Zuyu Yang
Author: Moses njagi Mwaniki
Author: Franklin l. Nobrega ORCID iD
Author: Yi Wu
Author: Hao Chen
Author: Joep De ligt
Author: Peter h. Sudmant
Author: Sanwen Huang
Author: Detlef Weigel
Author: Nicole Soranzo
Author: Vincenza Colonna
Author: Robert w. Williams
Author: Pjotr Prins

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