Building pangenome graphs

Erik Garrison^#¹, Andrea Guarracino^#^{2

3}, Simon Heumos^{4

5

6}, Flavia Villani², Zhigui Bao^{7

8}, Lorenzo Tattini^{9

10}, Jörg Hagmann¹¹, Sebastian Vorbrugg⁷, Santiago Marco-Sola^{12

13}, Christian Kubica⁷, David G Ashbrook², Kaisa Thorell¹⁴, Rachel L Rusholme-Pilcher¹⁵, Gianni Liti⁹, Emilio Rudbeck¹⁶, Agnieszka A Golicz¹⁷, Sven Nahnsen^{4

5

6

18}, Zuyu Yang¹⁹, Moses Njagi Mwaniki²⁰, Franklin L Nobrega²¹, Yi Wu²¹, Hao Chen²², Joep de Ligt²³, Peter H Sudmant²⁴, Sanwen Huang⁸, Detlef Weigel^{7

25}, Nicole Soranzo^{3

26

27

28

29}, Vincenza Colonna^{2

30}, Robert W Williams², Pjotr Prins²

Affiliations

¹ Department of Genetics, Genomics and Informatics, University of Tennessee Health Science Center, Memphis, TN, USA. egarris5@uthsc.edu.
² Department of Genetics, Genomics and Informatics, University of Tennessee Health Science Center, Memphis, TN, USA.
³ Human Technopole, Milan, Italy.
⁴ Quantitative Biology Center (QBiC) Tübingen, University of Tübingen, Tübingen, Germany.
⁵ Biomedical Data Science, Dept. of Computer Science, University of Tübingen, Tübingen, Germany.
⁶ M3 Research Center, University Hospital Tübingen, Tübingen, Germany.
⁷ Department of Molecular Biology, Max Planck Institute for Biology Tübingen, Tübingen, Germany.
⁸ Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China.
⁹ Université Côte d'Azur, CNRS, INSERM, IRCAN, Nice, France.
¹⁰ Data Science Department, EURECOM, Biot, France.
¹¹ Computomics, Tübingen, Germany.
¹² Computer Sciences Department, Barcelona Supercomputing Center, Barcelona, Spain.
¹³ Department of Computer Science, Universitat Politècnica de Catalunya, Barcelona, Spain.
¹⁴ Chemistry and Molecular Biology, Faculty of Science, University of Gothenburg, Gothenburg, Sweden.
¹⁵ Earlham Institute, Norwich Research Park, Norwich, UK.
¹⁶ Clinical Genomics Gothenburg, Bioinformatics and Data Centre, University of Gothenburg, Gothenburg, Sweden.
¹⁷ Department of Plant Breeding, Justus Liebig University Giessen, Giessen, Germany.
¹⁸ Institute for Bioinformatics and Medical Informatics (IBMI), Eberhard-Karls University of Tübingen, Tübingen, Germany.
¹⁹ The Institute of Environmental Science and Research, Wellington, New Zealand.
²⁰ Department of Computer Science, University of Pisa, Pisa, Italy.
²¹ School of Biological Sciences, Faculty of Environmental and Life Sciences, University of Southampton, Southampton, UK.
²² Department of Pharmacology, Addiction Science and Toxicology, University of Tennessee Health Science Center, Memphis, TN, USA.
²³ Hartwig Medical Foundation, Amsterdam, the Netherlands.
²⁴ Department of Integrative Biology, University of California Berkeley, Berkeley, CA, USA.
²⁵ Institute for Bioinformatics and Medical Informatics, University Tübingen, Tübingen, Germany.
²⁶ Wellcome Sanger Institute, Genome Campus, Hinxton, UK.
²⁷ National Institute for Health Research Blood and Transplant Research Unit in Donor Health and Genomics, University of Cambridge, Cambridge, UK.
²⁸ Department of Haematology, Cambridge Biomedical Campus, Cambridge, UK.
²⁹ British Heart Foundation Centre of Research Excellence, University of Cambridge, Cambridge, UK.
³⁰ Institute of Genetics and Biophysics, National Research Council, Naples, Italy.

^# Contributed equally.

PMID: 39433878
DOI: 10.1038/s41592-024-02430-3

Building pangenome graphs

Erik Garrison et al. Nat Methods. 2024 Nov.

. 2024 Nov;21(11):2008-2012.

doi: 10.1038/s41592-024-02430-3. Epub 2024 Oct 21.

Authors

Affiliations

¹ Department of Genetics, Genomics and Informatics, University of Tennessee Health Science Center, Memphis, TN, USA. egarris5@uthsc.edu.
² Department of Genetics, Genomics and Informatics, University of Tennessee Health Science Center, Memphis, TN, USA.
³ Human Technopole, Milan, Italy.
⁴ Quantitative Biology Center (QBiC) Tübingen, University of Tübingen, Tübingen, Germany.
⁵ Biomedical Data Science, Dept. of Computer Science, University of Tübingen, Tübingen, Germany.
⁶ M3 Research Center, University Hospital Tübingen, Tübingen, Germany.
⁷ Department of Molecular Biology, Max Planck Institute for Biology Tübingen, Tübingen, Germany.
⁸ Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China.
⁹ Université Côte d'Azur, CNRS, INSERM, IRCAN, Nice, France.
¹⁰ Data Science Department, EURECOM, Biot, France.
¹¹ Computomics, Tübingen, Germany.
¹² Computer Sciences Department, Barcelona Supercomputing Center, Barcelona, Spain.
¹³ Department of Computer Science, Universitat Politècnica de Catalunya, Barcelona, Spain.
¹⁴ Chemistry and Molecular Biology, Faculty of Science, University of Gothenburg, Gothenburg, Sweden.
¹⁵ Earlham Institute, Norwich Research Park, Norwich, UK.
¹⁶ Clinical Genomics Gothenburg, Bioinformatics and Data Centre, University of Gothenburg, Gothenburg, Sweden.
¹⁷ Department of Plant Breeding, Justus Liebig University Giessen, Giessen, Germany.
¹⁸ Institute for Bioinformatics and Medical Informatics (IBMI), Eberhard-Karls University of Tübingen, Tübingen, Germany.
¹⁹ The Institute of Environmental Science and Research, Wellington, New Zealand.
²⁰ Department of Computer Science, University of Pisa, Pisa, Italy.
²¹ School of Biological Sciences, Faculty of Environmental and Life Sciences, University of Southampton, Southampton, UK.
²² Department of Pharmacology, Addiction Science and Toxicology, University of Tennessee Health Science Center, Memphis, TN, USA.
²³ Hartwig Medical Foundation, Amsterdam, the Netherlands.
²⁴ Department of Integrative Biology, University of California Berkeley, Berkeley, CA, USA.
²⁵ Institute for Bioinformatics and Medical Informatics, University Tübingen, Tübingen, Germany.
²⁶ Wellcome Sanger Institute, Genome Campus, Hinxton, UK.
²⁷ National Institute for Health Research Blood and Transplant Research Unit in Donor Health and Genomics, University of Cambridge, Cambridge, UK.
²⁸ Department of Haematology, Cambridge Biomedical Campus, Cambridge, UK.
²⁹ British Heart Foundation Centre of Research Excellence, University of Cambridge, Cambridge, UK.
³⁰ Institute of Genetics and Biophysics, National Research Council, Naples, Italy.

^# Contributed equally.

PMID: 39433878
DOI: 10.1038/s41592-024-02430-3

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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Update of

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 DG, Thorell K, Rusholme-Pilcher RL, Liti G, Rudbeck E, Nahnsen S, Yang Z, Mwaniki MN, Nobrega FL, Wu Y, Chen H, de Ligt J, Sudmant PH, Soranzo N, Colonna V, Williams RW, Prins P. Garrison E, et al. bioRxiv [Preprint]. 2024 Oct 2:2023.04.05.535718. doi: 10.1101/2023.04.05.535718. bioRxiv. 2024. Update in: Nat Methods. 2024 Nov;21(11):2008-2012. doi: 10.1038/s41592-024-02430-3. PMID: 37066137 Free PMC article. Updated. Preprint.

References

1. Garrison, E. et al. Variation graph toolkit improves read mapping by representing genetic variation in the reference. Nature Biotechnol. 36, 875–879 (2018). - DOI
1. Paten, B., Novak, A. M., Eizenga, J. M. & Garrison, E. Genome graphs and the evolution of genome inference. Genome Res. 27, 665–676 (2017). - DOI - PubMed - PMC
1. Armstrong, J. et al. Progressive cactus is a multiple-genome aligner for the thousand-genome era. Nature 587, 246–251 (2020). - DOI - PubMed - PMC
1. Guarracino, A., Heumos, S., Nahnsen, S., Prins, P. & Garrison, E. ODGI: understanding pangenome graphs. Bioinformatics 38, 3319–3326 (2022). - DOI - PubMed - PMC
1. Li, H., Feng, X. & Chu, C. The design and construction of reference pangenome graphs with minigraph. Genome Biol. https://doi.org/10.1186/s13059-020-02168-z (2020).

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Building pangenome graphs

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Building pangenome graphs

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Abstract

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References

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