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The complete sequence of a human Y chromosome

View ORCID ProfileArang Rhie, Sergey Nurk, View ORCID ProfileMonika Cechova, View ORCID ProfileSavannah J. Hoyt, View ORCID ProfileDylan J. Taylor, View ORCID ProfileNicolas Altemose, View ORCID ProfilePaul W. Hook, View ORCID ProfileSergey Koren, Mikko Rautiainen, View ORCID ProfileIvan A. Alexandrov, View ORCID ProfileJamie Allen, View ORCID ProfileMobin Asri, Andrey V. Bzikadze, View ORCID ProfileNae-Chyun Chen, View ORCID ProfileChen-Shan Chin, View ORCID ProfileMark Diekhans, View ORCID ProfilePaul Flicek, View ORCID ProfileGiulio Formenti, View ORCID ProfileArkarachai Fungtammasan, View ORCID ProfileCarlos Garcia Giron, View ORCID ProfileErik Garrison, View ORCID ProfileAriel Gershman, View ORCID ProfileJennifer Gerton, View ORCID ProfilePatrick G.S. Grady, View ORCID ProfileAndrea Guarracino, View ORCID ProfileLeanne Haggerty, View ORCID ProfileReza Halabian, View ORCID ProfileNancy F. Hansen, View ORCID ProfileRobert Harris, View ORCID ProfileGabrielle A. Hartley, View ORCID ProfileWilliam T. Harvey, View ORCID ProfileMarina Haukness, View ORCID ProfileJakob Heinz, View ORCID ProfileThibaut Hourlier, View ORCID ProfileRobert M. Hubley, View ORCID ProfileSarah E. Hunt, View ORCID ProfileStephen Hwang, View ORCID ProfileMiten Jain, View ORCID ProfileRupesh K. Kesharwani, View ORCID ProfileAlexandra P. Lewis, View ORCID ProfileHeng Li, View ORCID ProfileGlennis A. Logsdon, View ORCID ProfileJulian K. Lucas, View ORCID ProfileWojciech Makalowski, Christopher Markovic, View ORCID ProfileFergal J. Martin, View ORCID ProfileAnn M. Mc Cartney, View ORCID ProfileRajiv C. McCoy, View ORCID ProfileJennifer McDaniel, Brandy M. McNulty, View ORCID ProfilePaul Medvedev, View ORCID ProfileAlla Mikheenko, View ORCID ProfileKatherine M. Munson, View ORCID ProfileTerence D. Murphy, Hugh E. Olsen, View ORCID ProfileNathan D. Olson, View ORCID ProfileLuis F. Paulin, View ORCID ProfileDavid Porubsky, View ORCID ProfileTamara Potapova, View ORCID ProfileFedor Ryabov, View ORCID ProfileSteven L. Salzberg, View ORCID ProfileMichael E.G. Sauria, View ORCID ProfileFritz J. Sedlazeck, View ORCID ProfileKishwar Shafin, Valery A. Shepelev, View ORCID ProfileAlaina Shumate, View ORCID ProfileJessica M. Storer, View ORCID ProfileLikhitha Surapaneni, View ORCID ProfileAngela M. Taravella Oill, View ORCID ProfileFrançoise Thibaud-Nissen, View ORCID ProfileWinston Timp, View ORCID ProfileMarta Tomaszkiewicz, View ORCID ProfileMitchell R. Vollger, Brian P. Walenz, View ORCID ProfileAllison C. Watwood, View ORCID ProfileMatthias H. Weissensteiner, View ORCID ProfileAaron M. Wenger, View ORCID ProfileMelissa A. Wilson, View ORCID ProfileSamantha Zarate, Yiming Zhu, View ORCID ProfileJustin M. Zook, View ORCID ProfileEvan E. Eichler, View ORCID ProfileRachel O’Neill, View ORCID ProfileMichael C. Schatz, View ORCID ProfileKaren H. Miga, View ORCID ProfileKateryna D. Makova, View ORCID ProfileAdam M. Phillippy
doi: https://doi.org/10.1101/2022.12.01.518724
Arang Rhie
1Genome Informatics Section, Computational and Statistical Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
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  • ORCID record for Arang Rhie
Sergey Nurk
1Genome Informatics Section, Computational and Statistical Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
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Monika Cechova
2Faculty of Informatics, Masaryk University, Czech republic
3Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, CA, USA
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Savannah J. Hoyt
4Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT, USA
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  • ORCID record for Savannah J. Hoyt
Dylan J. Taylor
5Department of Biology, Johns Hopkins University, Baltimore, MD, USA
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Nicolas Altemose
6Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
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Paul W. Hook
7Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, USA
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Sergey Koren
1Genome Informatics Section, Computational and Statistical Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
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Mikko Rautiainen
1Genome Informatics Section, Computational and Statistical Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
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Ivan A. Alexandrov
8Federal Research Center of Biotechnology of the Russian Academy of Sciences, Moscow, Russia
9Center for Algorithmic Biotechnology, Saint Petersburg State University, Russia
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Jamie Allen
10European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, United Kingdom
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  • ORCID record for Jamie Allen
Mobin Asri
11UC Santa Cruz Genomics Institute, University of California Santa Cruz, Santa Cruz, CA, USA
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Andrey V. Bzikadze
12Graduate Program in Bioinformatics and Systems Biology, University of California, San Diego, CA, USA
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Nae-Chyun Chen
13Department of Computer Science, Johns Hopkins University, Baltimore, MD, USA
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Chen-Shan Chin
14Sema4, OpCo, Inc, Stamford, CT, USA
15Foundation of Biological Data Science, Belmont, CA, USA
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Mark Diekhans
11UC Santa Cruz Genomics Institute, University of California Santa Cruz, Santa Cruz, CA, USA
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Paul Flicek
10European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, United Kingdom
16Department of Genetics, University of Cambridge, Cambridge, United Kingdom
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Giulio Formenti
17The Rockefeller University, New York, NY, USA
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Arkarachai Fungtammasan
18DNAnexus, Mountain View, CA, USA
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Carlos Garcia Giron
10European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, United Kingdom
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Erik Garrison
19Department of Genetics, Genomics and Informatics, University of Tennessee Health Science Center, Memphis, Tennessee, USA
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  • ORCID record for Erik Garrison
Ariel Gershman
7Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, USA
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Jennifer Gerton
20Stowers Institute for Medical Research, Kansas City, MO, USA
21University of Kansas Medical Center, Kansas City, MO, USA
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Patrick G.S. Grady
4Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT, USA
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Andrea Guarracino
22Genomics Research Centre, Human Technopole, Viale Rita Levi-Montalcini 1, Milan, Italy
19Department of Genetics, Genomics and Informatics, University of Tennessee Health Science Center, Memphis, Tennessee, USA
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Leanne Haggerty
10European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, United Kingdom
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Reza Halabian
23Institute of Bioinformatics, Faculty of Medicine, University of Münster, Münster, Germany
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Nancy F. Hansen
24Cancer Genetics and Comparative Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
1Genome Informatics Section, Computational and Statistical Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
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Robert Harris
25Department of Biology, Pennsylvania State University, University Park, PA, USA
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Gabrielle A. Hartley
4Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT, USA
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William T. Harvey
26Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
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Marina Haukness
11UC Santa Cruz Genomics Institute, University of California Santa Cruz, Santa Cruz, CA, USA
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Jakob Heinz
7Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, USA
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Thibaut Hourlier
10European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, United Kingdom
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Robert M. Hubley
27Institute for Systems Biology, Seattle, WA, USA
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Sarah E. Hunt
10European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, United Kingdom
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Stephen Hwang
28XDBio Program, Johns Hopkins University, Baltimore, MD, USA
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Miten Jain
29Department of Bioengineering, Department of Physics, Northeastern University, Boston, MA, USA
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  • ORCID record for Miten Jain
Rupesh K. Kesharwani
30Human Genome Sequencing Center, Baylor College of Medicine, One Baylor Plaza, Houston, TX, USA
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Alexandra P. Lewis
26Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
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Heng Li
31Department of data sciences, Dana-Farber Cancer Institute, Boston, MA, USA
32Department of biomedical informatics, Harvard Medical School, Boston, MA, USA
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Glennis A. Logsdon
26Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
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Julian K. Lucas
3Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, CA, USA
11UC Santa Cruz Genomics Institute, University of California Santa Cruz, Santa Cruz, CA, USA
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Wojciech Makalowski
23Institute of Bioinformatics, Faculty of Medicine, University of Münster, Münster, Germany
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Christopher Markovic
33Genome Technology Access Center at the McDonnell Genome Institute (GTAC@MGI) Washington University, St. Louis, MO, USA
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Fergal J. Martin
10European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, United Kingdom
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Ann M. Mc Cartney
1Genome Informatics Section, Computational and Statistical Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
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Rajiv C. McCoy
5Department of Biology, Johns Hopkins University, Baltimore, MD, USA
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Jennifer McDaniel
34Biosystems and Biomaterials Division, National Institute of Standards and Technology, Gaithersburg, MD, USA
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  • ORCID record for Jennifer McDaniel
Brandy M. McNulty
3Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, CA, USA
11UC Santa Cruz Genomics Institute, University of California Santa Cruz, Santa Cruz, CA, USA
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Paul Medvedev
35Department of Computer Science and Engineering, Pennsylvania State University, University Park, PA, USA
36Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, PA, USA
37Center for Computational Biology and Bioinformatics, Pennsylvania State University, University Park, PA, USA
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Alla Mikheenko
9Center for Algorithmic Biotechnology, Saint Petersburg State University, Russia
38UCL Queen Square Institute of Neurology, UCL, London, UK
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Katherine M. Munson
26Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
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Terence D. Murphy
39National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
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Hugh E. Olsen
3Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, CA, USA
11UC Santa Cruz Genomics Institute, University of California Santa Cruz, Santa Cruz, CA, USA
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Nathan D. Olson
34Biosystems and Biomaterials Division, National Institute of Standards and Technology, Gaithersburg, MD, USA
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  • ORCID record for Nathan D. Olson
Luis F. Paulin
30Human Genome Sequencing Center, Baylor College of Medicine, One Baylor Plaza, Houston, TX, USA
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David Porubsky
26Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
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Tamara Potapova
20Stowers Institute for Medical Research, Kansas City, MO, USA
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Fedor Ryabov
40Masters Program in National Research University Higher School of Economics, Moscow, Russia
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Steven L. Salzberg
41Departments of Biomedical Engineering, Computer Science, and Biostatistics, Johns Hopkins University, Baltimore, MD
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Michael E.G. Sauria
5Department of Biology, Johns Hopkins University, Baltimore, MD, USA
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Fritz J. Sedlazeck
30Human Genome Sequencing Center, Baylor College of Medicine, One Baylor Plaza, Houston, TX, USA
42Department of Computer Science, Rice University, Houston, TX, USA
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Kishwar Shafin
43Google Inc, 1600 Amphitheatre Pkwy, Mountain View, CA, USA
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Valery A. Shepelev
44Institute of Molecular Genetics, Moscow, Russia
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Alaina Shumate
7Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, USA
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Jessica M. Storer
27Institute for Systems Biology, Seattle, WA, USA
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Likhitha Surapaneni
10European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, United Kingdom
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Angela M. Taravella Oill
45Center for Evolution and Medicine, School of Life Sciences, Arizona State University, Tempe, AZ, USA
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Françoise Thibaud-Nissen
39National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
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Winston Timp
7Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, USA
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Marta Tomaszkiewicz
25Department of Biology, Pennsylvania State University, University Park, PA, USA
46Department of Biomedical Engineering, Pennsylvania State University, State College, PA, USA
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Mitchell R. Vollger
26Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
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Brian P. Walenz
1Genome Informatics Section, Computational and Statistical Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
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Allison C. Watwood
25Department of Biology, Pennsylvania State University, University Park, PA, USA
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Matthias H. Weissensteiner
25Department of Biology, Pennsylvania State University, University Park, PA, USA
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Aaron M. Wenger
47Pacific Biosciences, Menlo Park, CA, USA
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Melissa A. Wilson
45Center for Evolution and Medicine, School of Life Sciences, Arizona State University, Tempe, AZ, USA
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  • ORCID record for Melissa A. Wilson
Samantha Zarate
13Department of Computer Science, Johns Hopkins University, Baltimore, MD, USA
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Yiming Zhu
30Human Genome Sequencing Center, Baylor College of Medicine, One Baylor Plaza, Houston, TX, USA
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Justin M. Zook
34Biosystems and Biomaterials Division, National Institute of Standards and Technology, Gaithersburg, MD, USA
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Evan E. Eichler
26Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
48Investigator, Howard Hughes Medical Institute, University of Washington, Seattle, WA, USA
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Rachel O’Neill
4Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT, USA
49Institute for Systems Genomics, University of Connecticut, Storrs, CT, USA
50Department of Genetics and Genome Sciences, UConn Health, Farmington, CT, USA
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Michael C. Schatz
13Department of Computer Science, Johns Hopkins University, Baltimore, MD, USA
5Department of Biology, Johns Hopkins University, Baltimore, MD, USA
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Karen H. Miga
3Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, CA, USA
11UC Santa Cruz Genomics Institute, University of California Santa Cruz, Santa Cruz, CA, USA
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Kateryna D. Makova
25Department of Biology, Pennsylvania State University, University Park, PA, USA
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Adam M. Phillippy
1Genome Informatics Section, Computational and Statistical Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
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  • For correspondence: adam.phillippy@nih.gov
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Abstract

The human Y chromosome has been notoriously difficult to sequence and assemble because of its complex repeat structure including long palindromes, tandem repeats, and segmental duplications. As a result, more than half of the Y chromosome is missing from the GRCh38 reference sequence and it remains the last human chromosome to be finished. Here, the Telomere-to-Telomere (T2T) consortium presents the complete 62,460,029 base pair sequence of a human Y chromosome from the HG002 genome (T2T-Y) that corrects multiple errors in GRCh38-Y and adds over 30 million base pairs of sequence to the reference, revealing the complete ampliconic structures of TSPY, DAZ, and RBMY; 42 additional protein-coding genes, mostly from the TSPY gene family; and an alternating pattern of human satellite 1 and 3 blocks in the heterochromatic Yq12 region. We have combined T2T-Y with a prior assembly of the CHM13 genome and mapped available population variation, clinical variants, and functional genomics data to produce a complete and comprehensive reference sequence for all 24 human chromosomes.

Competing Interest Statement

S.N. is an employee of Oxford Nanopore Technologies; A.F. is an employee of DNAnexus; C.-S.C. is an employee of Sema4 OpCo Inc.; N.-C.C. is an employee of Exai Bio; L.F.P. receives research support from Genetech; F.J.S. receives research support from Pacific Biosciences, Oxford Nanopore Technologies, Illumina, and Genetech; K.S. is an employee of Google LLC and owns Alphabet stock as part of the standard compensation package; W.T. has two patents (8,748,091 and 8,394,584) licensed to Oxford Nanopore Technologies; E.E.E. is a scientific advisory board member of Variant Bio, Inc.

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The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. This article is a US Government work. It is not subject to copyright under 17 USC 105 and is also made available for use under a CC0 license.
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The complete sequence of a human Y chromosome
Arang Rhie, Sergey Nurk, Monika Cechova, Savannah J. Hoyt, Dylan J. Taylor, Nicolas Altemose, Paul W. Hook, Sergey Koren, Mikko Rautiainen, Ivan A. Alexandrov, Jamie Allen, Mobin Asri, Andrey V. Bzikadze, Nae-Chyun Chen, Chen-Shan Chin, Mark Diekhans, Paul Flicek, Giulio Formenti, Arkarachai Fungtammasan, Carlos Garcia Giron, Erik Garrison, Ariel Gershman, Jennifer Gerton, Patrick G.S. Grady, Andrea Guarracino, Leanne Haggerty, Reza Halabian, Nancy F. Hansen, Robert Harris, Gabrielle A. Hartley, William T. Harvey, Marina Haukness, Jakob Heinz, Thibaut Hourlier, Robert M. Hubley, Sarah E. Hunt, Stephen Hwang, Miten Jain, Rupesh K. Kesharwani, Alexandra P. Lewis, Heng Li, Glennis A. Logsdon, Julian K. Lucas, Wojciech Makalowski, Christopher Markovic, Fergal J. Martin, Ann M. Mc Cartney, Rajiv C. McCoy, Jennifer McDaniel, Brandy M. McNulty, Paul Medvedev, Alla Mikheenko, Katherine M. Munson, Terence D. Murphy, Hugh E. Olsen, Nathan D. Olson, Luis F. Paulin, David Porubsky, Tamara Potapova, Fedor Ryabov, Steven L. Salzberg, Michael E.G. Sauria, Fritz J. Sedlazeck, Kishwar Shafin, Valery A. Shepelev, Alaina Shumate, Jessica M. Storer, Likhitha Surapaneni, Angela M. Taravella Oill, Françoise Thibaud-Nissen, Winston Timp, Marta Tomaszkiewicz, Mitchell R. Vollger, Brian P. Walenz, Allison C. Watwood, Matthias H. Weissensteiner, Aaron M. Wenger, Melissa A. Wilson, Samantha Zarate, Yiming Zhu, Justin M. Zook, Evan E. Eichler, Rachel O’Neill, Michael C. Schatz, Karen H. Miga, Kateryna D. Makova, Adam M. Phillippy
bioRxiv 2022.12.01.518724; doi: https://doi.org/10.1101/2022.12.01.518724
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The complete sequence of a human Y chromosome
Arang Rhie, Sergey Nurk, Monika Cechova, Savannah J. Hoyt, Dylan J. Taylor, Nicolas Altemose, Paul W. Hook, Sergey Koren, Mikko Rautiainen, Ivan A. Alexandrov, Jamie Allen, Mobin Asri, Andrey V. Bzikadze, Nae-Chyun Chen, Chen-Shan Chin, Mark Diekhans, Paul Flicek, Giulio Formenti, Arkarachai Fungtammasan, Carlos Garcia Giron, Erik Garrison, Ariel Gershman, Jennifer Gerton, Patrick G.S. Grady, Andrea Guarracino, Leanne Haggerty, Reza Halabian, Nancy F. Hansen, Robert Harris, Gabrielle A. Hartley, William T. Harvey, Marina Haukness, Jakob Heinz, Thibaut Hourlier, Robert M. Hubley, Sarah E. Hunt, Stephen Hwang, Miten Jain, Rupesh K. Kesharwani, Alexandra P. Lewis, Heng Li, Glennis A. Logsdon, Julian K. Lucas, Wojciech Makalowski, Christopher Markovic, Fergal J. Martin, Ann M. Mc Cartney, Rajiv C. McCoy, Jennifer McDaniel, Brandy M. McNulty, Paul Medvedev, Alla Mikheenko, Katherine M. Munson, Terence D. Murphy, Hugh E. Olsen, Nathan D. Olson, Luis F. Paulin, David Porubsky, Tamara Potapova, Fedor Ryabov, Steven L. Salzberg, Michael E.G. Sauria, Fritz J. Sedlazeck, Kishwar Shafin, Valery A. Shepelev, Alaina Shumate, Jessica M. Storer, Likhitha Surapaneni, Angela M. Taravella Oill, Françoise Thibaud-Nissen, Winston Timp, Marta Tomaszkiewicz, Mitchell R. Vollger, Brian P. Walenz, Allison C. Watwood, Matthias H. Weissensteiner, Aaron M. Wenger, Melissa A. Wilson, Samantha Zarate, Yiming Zhu, Justin M. Zook, Evan E. Eichler, Rachel O’Neill, Michael C. Schatz, Karen H. Miga, Kateryna D. Makova, Adam M. Phillippy
bioRxiv 2022.12.01.518724; doi: https://doi.org/10.1101/2022.12.01.518724

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