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Automated assembly of high-quality diploid human reference genomes

View ORCID ProfileErich D. Jarvis, View ORCID ProfileGiulio Formenti, View ORCID ProfileArang Rhie, View ORCID ProfileAndrea Guarracino, Chentao Yang, Jonathan Wood, Alan Tracey, Francoise Thibaud-Nissen, View ORCID ProfileMitchell R. Vollger, David Porubsky, Haoyu Cheng, Mobin Asri, Glennis A. Logsdon, Paolo Carnevali, Mark J.P. Chaisson, Chen-Shan Chin, Sarah Cody, View ORCID ProfileJoanna Collins, View ORCID ProfilePeter Ebert, View ORCID ProfileMerly Escalona, View ORCID ProfileOlivier Fedrigo, Robert S. Fulton, Lucinda L. Fulton, Shilpa Garg, Jay Ghurye, View ORCID ProfileEdward Green, Ira Hall, William Harvey, Patrick Hasenfeld, Alex Hastie, Marina Haukness, Miten Jain, View ORCID ProfileMelanie Kirsche, Mikhail Kolmogorov, Jan O. Korbel, Sergey Koren, Jonas Korlach, Joyce Lee, View ORCID ProfileDaofeng Li, Tina Lindsay, Julian Lucas, Feng Luo, Tobias Marschall, Jennifer McDaniel, Fan Nie, Hugh E. Olsen, Nathan D. Olson, View ORCID ProfileTrevor Pesout, Daniela Puiu, Allison Regier, Jue Ruan, Steven L. Salzberg, Ashley D. Sanders, Michael C. Schatz, Anthony Schmitt, Valerie A. Schneider, Siddarth Selvaraj, View ORCID ProfileKishwar Shafin, Alaina Shumate, Catherine Stober, James Torrance, Justin Wagner, Jianxin Wang, Aaron Wenger, Chuanle Xiao, Aleksey V. Zimin, Guojie Zhang, Ting Wang, View ORCID ProfileHeng Li, View ORCID ProfileErik Garrison, David Haussler, View ORCID ProfileJustin M. Zook, View ORCID ProfileEvan E. Eichler, Adam M. Phillippy, Benedict Paten, View ORCID ProfileKerstin Howe, Karen H. Miga, Human Pangenome Reference Consortium
doi: https://doi.org/10.1101/2022.03.06.483034
Erich D. Jarvis
1Vertebrate Genome Laboratory, The Rockefeller University, New York, NY, USA
2Investigator, Howard Hughes Medical Institute, Chevy Chase, MD, USA
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  • ORCID record for Erich D. Jarvis
  • For correspondence: ejarvis@rockefeller.edu gformenti@rockefeller.edu kj2@sanger.ac.uk khmiga@ucsc.edu
Giulio Formenti
1Vertebrate Genome Laboratory, The Rockefeller University, New York, NY, USA
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  • For correspondence: ejarvis@rockefeller.edu gformenti@rockefeller.edu kj2@sanger.ac.uk khmiga@ucsc.edu
Arang Rhie
3National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
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Andrea Guarracino
4Genomics Research Centre, Human Technopole, Viale Rita Levi-Montalcini, Milano MI, Italy
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Chentao Yang
5BGI-Shenzhen, Shenzhen, China
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Jonathan Wood
6Tree of Life, Wellcome Sanger Institute, Cambridge, MA, USA
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Alan Tracey
6Tree of Life, Wellcome Sanger Institute, Cambridge, MA, USA
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Francoise Thibaud-Nissen
7NCBI, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
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Mitchell R. Vollger
8Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
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David Porubsky
8Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
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Haoyu Cheng
9Department of Data Sciences, Dana-Farber Cancer Institute, Boston, MA, USA
10Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
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Mobin Asri
11UC Santa Cruz Genomics Institute, University of California Santa Cruz, CA, USA
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Glennis A. Logsdon
8Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
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Paolo Carnevali
12Chan Zuckerberg Initiative, Redwood City, CA, USA
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Mark J.P. Chaisson
13Quantitative and Computational Biology, University of Southern California, Los Angeles, CA, USA
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Chen-Shan Chin
14Foundation for Biological Data Science, Belmont, CA, USA
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Sarah Cody
15McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO, USA
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Joanna Collins
6Tree of Life, Wellcome Sanger Institute, Cambridge, MA, USA
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Peter Ebert
16Institute for Medical Biometry and Bioinformatics, Medical Faculty, Heinrich Heine University, Düsseldorf, Germany
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Merly Escalona
17Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, CA, USA
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Olivier Fedrigo
1Vertebrate Genome Laboratory, The Rockefeller University, New York, NY, USA
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Robert S. Fulton
15McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO, USA
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Lucinda L. Fulton
15McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO, USA
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Shilpa Garg
18Department of Biology, University of Copenhagen, Copenhagen Denmark
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Jay Ghurye
19Dovetail Genomics, Scotts Valley, CA, USA
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Edward Green
19Dovetail Genomics, Scotts Valley, CA, USA
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Ira Hall
20Yale School of Medicine, New Haven, CT, USA
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William Harvey
8Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
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Patrick Hasenfeld
21Genome Biology, European Molecular Biology Laboratory, Heidelberg, Germany
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Alex Hastie
22Bionano Genomics, San Diego, CA, USA
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Marina Haukness
11UC Santa Cruz Genomics Institute, University of California Santa Cruz, CA, USA
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Miten Jain
11UC Santa Cruz Genomics Institute, University of California Santa Cruz, CA, USA
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Melanie Kirsche
23Department of Computer Science, Johns Hopkins University, Baltimore, MD USA
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Mikhail Kolmogorov
24Department of Computer Science and Engineering, University of California San Diego, La Jolla, CA, USA
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Jan O. Korbel
21Genome Biology, European Molecular Biology Laboratory, Heidelberg, Germany
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Sergey Koren
3National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
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Jonas Korlach
25Pacific Biosciences, Menlo Park, CA, USA
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Joyce Lee
22Bionano Genomics, San Diego, CA, USA
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Daofeng Li
26Department of Genetics, Washington University School of Medicine, St. Louis, MO, USA
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Tina Lindsay
15McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO, USA
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Julian Lucas
11UC Santa Cruz Genomics Institute, University of California Santa Cruz, CA, USA
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Feng Luo
27School of Computing, Clemson University, Clemson, SC, USA
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Tobias Marschall
16Institute for Medical Biometry and Bioinformatics, Medical Faculty, Heinrich Heine University, Düsseldorf, Germany
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Jennifer McDaniel
28Material Measurement Laboratory, National Institute of Standards and Technology, Gaithersburg, MD, USA
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Fan Nie
29Hunan Provincial Key Lab on Bioinformatics, School of Computer Science and Engineering, Central South University, Changsha, China
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Hugh E. Olsen
11UC Santa Cruz Genomics Institute, University of California Santa Cruz, CA, USA
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Nathan D. Olson
28Material Measurement Laboratory, National Institute of Standards and Technology, Gaithersburg, MD, USA
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Trevor Pesout
11UC Santa Cruz Genomics Institute, University of California Santa Cruz, CA, USA
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Daniela Puiu
30Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, USA
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Allison Regier
31DNAnexus, Mountain View, CA, USA
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Jue Ruan
32Agricultural Genomics Institute, Chinese Academy of Agricultural Sciences, Shenzhen, China
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Steven L. Salzberg
30Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, USA
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Ashley D. Sanders
33Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany
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Michael C. Schatz
23Department of Computer Science, Johns Hopkins University, Baltimore, MD USA
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Anthony Schmitt
34Arima Genomics, San Diego, CA, USA
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Valerie A. Schneider
7NCBI, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
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Siddarth Selvaraj
34Arima Genomics, San Diego, CA, USA
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Kishwar Shafin
11UC Santa Cruz Genomics Institute, University of California Santa Cruz, CA, USA
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Alaina Shumate
30Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, USA
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Catherine Stober
21Genome Biology, European Molecular Biology Laboratory, Heidelberg, Germany
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James Torrance
6Tree of Life, Wellcome Sanger Institute, Cambridge, MA, USA
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Justin Wagner
28Material Measurement Laboratory, National Institute of Standards and Technology, Gaithersburg, MD, USA
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Jianxin Wang
29Hunan Provincial Key Lab on Bioinformatics, School of Computer Science and Engineering, Central South University, Changsha, China
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Aaron Wenger
25Pacific Biosciences, Menlo Park, CA, USA
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Chuanle Xiao
35State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou, China
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Aleksey V. Zimin
30Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, USA
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Guojie Zhang
36Kunming Institute of Zoology, Chinese Academy of Sciences, China
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Ting Wang
15McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO, USA
26Department of Genetics, Washington University School of Medicine, St. Louis, MO, USA
37Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO, USA
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Heng Li
9Department of Data Sciences, Dana-Farber Cancer Institute, Boston, MA, USA
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Erik Garrison
38Department of Genetics, Genomics and Informatics, University of Tennessee Health Science Center, Memphis, TN, USA
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David Haussler
39Department of Ecology and Evolutionary Biology, University of California Santa Cruz, Santa Cruz, CA, USA
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Justin M. Zook
28Material Measurement Laboratory, National Institute of Standards and Technology, Gaithersburg, MD, USA
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Evan E. Eichler
8Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
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Adam M. Phillippy
3National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
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Benedict Paten
11UC Santa Cruz Genomics Institute, University of California Santa Cruz, CA, USA
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Kerstin Howe
6Tree of Life, Wellcome Sanger Institute, Cambridge, MA, USA
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  • For correspondence: ejarvis@rockefeller.edu gformenti@rockefeller.edu kj2@sanger.ac.uk khmiga@ucsc.edu
Karen H. Miga
11UC Santa Cruz Genomics Institute, University of California Santa Cruz, CA, USA
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  • For correspondence: ejarvis@rockefeller.edu gformenti@rockefeller.edu kj2@sanger.ac.uk khmiga@ucsc.edu
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Abstract

The current human reference genome, GRCh38, represents over 20 years of effort to generate a high-quality assembly, which has greatly benefited society1, 2. However, it still has many gaps and errors, and does not represent a biological human genome since it is a blend of multiple individuals3, 4. Recently, a high-quality telomere-to-telomere reference genome, CHM13, was generated with the latest long-read technologies, but it was derived from a hydatidiform mole cell line with a duplicate genome, and is thus nearly homozygous5. To address these limitations, the Human Pangenome Reference Consortium (HPRC) recently formed with the goal of creating a collection of high-quality, cost-effective, diploid genome assemblies for a pangenome reference that represents human genetic diversity6. Here, in our first scientific report, we determined which combination of current genome sequencing and automated assembly approaches yields the most complete, accurate, and cost-effective diploid genome assemblies with minimal manual curation. Approaches that used highly accurate long reads and parent-child data to sort haplotypes during assembly outperformed those that did not. Developing a combination of all the top performing methods, we generated our first high-quality diploid reference assembly, containing only ∼4 gaps (range 0-12) per chromosome, most within + 1% of CHM13’s length. Nearly 1/4th of protein coding genes have synonymous amino acid changes between haplotypes, and centromeric regions showed the highest density of variation. Our findings serve as a foundation for assembling near-complete diploid human genomes at the scale required for constructing a human pangenome reference that captures all genetic variation from single nucleotides to large structural rearrangements.

Competing Interest Statement

E.E.E. is a scientific advisory board (SAB) member of Variant Bio, Inc. J.L. and A.H. are former and current employees and shareholders of Bionano Genomics, Inc respectively.

Footnotes

  • ↵* co-first authors

  • https://github.com/human-pangenomics/HG002_Data_Freeze_v1.0

  • https://s3-us-west-2.amazonaws.com/human-pangenomics/index.html?prefix=

Copyright 
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY 4.0 International license.
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Automated assembly of high-quality diploid human reference genomes
Erich D. Jarvis, Giulio Formenti, Arang Rhie, Andrea Guarracino, Chentao Yang, Jonathan Wood, Alan Tracey, Francoise Thibaud-Nissen, Mitchell R. Vollger, David Porubsky, Haoyu Cheng, Mobin Asri, Glennis A. Logsdon, Paolo Carnevali, Mark J.P. Chaisson, Chen-Shan Chin, Sarah Cody, Joanna Collins, Peter Ebert, Merly Escalona, Olivier Fedrigo, Robert S. Fulton, Lucinda L. Fulton, Shilpa Garg, Jay Ghurye, Edward Green, Ira Hall, William Harvey, Patrick Hasenfeld, Alex Hastie, Marina Haukness, Miten Jain, Melanie Kirsche, Mikhail Kolmogorov, Jan O. Korbel, Sergey Koren, Jonas Korlach, Joyce Lee, Daofeng Li, Tina Lindsay, Julian Lucas, Feng Luo, Tobias Marschall, Jennifer McDaniel, Fan Nie, Hugh E. Olsen, Nathan D. Olson, Trevor Pesout, Daniela Puiu, Allison Regier, Jue Ruan, Steven L. Salzberg, Ashley D. Sanders, Michael C. Schatz, Anthony Schmitt, Valerie A. Schneider, Siddarth Selvaraj, Kishwar Shafin, Alaina Shumate, Catherine Stober, James Torrance, Justin Wagner, Jianxin Wang, Aaron Wenger, Chuanle Xiao, Aleksey V. Zimin, Guojie Zhang, Ting Wang, Heng Li, Erik Garrison, David Haussler, Justin M. Zook, Evan E. Eichler, Adam M. Phillippy, Benedict Paten, Kerstin Howe, Karen H. Miga, Human Pangenome Reference Consortium
bioRxiv 2022.03.06.483034; doi: https://doi.org/10.1101/2022.03.06.483034
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Automated assembly of high-quality diploid human reference genomes
Erich D. Jarvis, Giulio Formenti, Arang Rhie, Andrea Guarracino, Chentao Yang, Jonathan Wood, Alan Tracey, Francoise Thibaud-Nissen, Mitchell R. Vollger, David Porubsky, Haoyu Cheng, Mobin Asri, Glennis A. Logsdon, Paolo Carnevali, Mark J.P. Chaisson, Chen-Shan Chin, Sarah Cody, Joanna Collins, Peter Ebert, Merly Escalona, Olivier Fedrigo, Robert S. Fulton, Lucinda L. Fulton, Shilpa Garg, Jay Ghurye, Edward Green, Ira Hall, William Harvey, Patrick Hasenfeld, Alex Hastie, Marina Haukness, Miten Jain, Melanie Kirsche, Mikhail Kolmogorov, Jan O. Korbel, Sergey Koren, Jonas Korlach, Joyce Lee, Daofeng Li, Tina Lindsay, Julian Lucas, Feng Luo, Tobias Marschall, Jennifer McDaniel, Fan Nie, Hugh E. Olsen, Nathan D. Olson, Trevor Pesout, Daniela Puiu, Allison Regier, Jue Ruan, Steven L. Salzberg, Ashley D. Sanders, Michael C. Schatz, Anthony Schmitt, Valerie A. Schneider, Siddarth Selvaraj, Kishwar Shafin, Alaina Shumate, Catherine Stober, James Torrance, Justin Wagner, Jianxin Wang, Aaron Wenger, Chuanle Xiao, Aleksey V. Zimin, Guojie Zhang, Ting Wang, Heng Li, Erik Garrison, David Haussler, Justin M. Zook, Evan E. Eichler, Adam M. Phillippy, Benedict Paten, Kerstin Howe, Karen H. Miga, Human Pangenome Reference Consortium
bioRxiv 2022.03.06.483034; doi: https://doi.org/10.1101/2022.03.06.483034

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