{
  "abstract": "Human genome resequencing typically involves mapping reads to a reference genome to call variants; however, this approach suffers from both technical and reference biases, leaving many duplicated and structurally polymorphic regions of the genome unmapped. Consequently, existing variant benchmarks, generated by the same methods, fail to assess these complex regions. To address this limitation, we present a telomere-to-telomere genome benchmark that achieves near-perfect accuracy (i.e. no detectable errors) across 99.4% of the complete, diploid HG002 genome. This benchmark adds 701.4 Mb of autosomal sequence and both sex chromosomes (216.8 Mb), totaling 15.3% of the genome that was absent from prior benchmarks. We also provide a diploid annotation of genes, transposable elements, segmental duplications, and satellite repeats, including 39,144 protein-coding genes across both haplotypes. To facilitate application of the benchmark, we developed tools for measuring the accuracy of sequencing reads, phased variant call sets, and genome assemblies against a diploid reference. Genome-wide analyses show that state-of-the-art de novo assembly methods resolve 2-7% more sequence and outperform variant calling accuracy by an order of magnitude, yielding just one error per 100 kb across 99.9% of the benchmark regions. Adoption of genome-based benchmarking is expected to accelerate the development of cost-effective methods for complete genome sequencing, expanding the reach of genomic medicine to the entire genome and enabling a new era of personalized genomics.",
  "abstract_shown": true,
  "affiliations": [
    "Genome Informatics Section, Center for Genomics and Data Science Research, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA",
    "Material Measurement Laboratory, National Institute of Standards and Technology, Gaithersburg, MD, USA",
    "Department of Computer Science, Johns Hopkins University, Baltimore, MD, USA; Center for Computational Biology, Johns Hopkins University, Baltimore, MD, USA",
    "Department of Computer Science, Johns Hopkins University, Baltimore, MD, USA",
    "University of California, Santa Cruz Genomics Institute, University of California, Santa Cruz, Santa Cruz, CA, USA",
    "UC Santa Cruz Genomics Institute, University of California, Santa Cruz, CA, USA",
    "Department of Genetics, Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA",
    "Division of Medical Genetics, Department of Medicine, University of Washington School of Medicine, Seattle, WA, USA",
    "Division of Medical Genetics, University of Washington School of Medicine, Seattle, WA, USA",
    "Institute for Systems Genomics, University of Connecticut, Storrs, CT, USA",
    "Department of Computer Science, Old Dominion University, Norfolk, VA, USA",
    "Department of Genetics, School of Medicine, Stanford University, Palo Alto, CA, USA; Chan Zuckerberg Biohub, San Francisco, CA, USA",
    "Chan Zuckerberg Biohub, San Francisco, San Francisco, CA, USA",
    "Department of Genetics, School of Medicine, Stanford University, Palo Alto, CA, USA",
    "UC Santa Cruz Genomics Institute, Santa Cruz, CA, USA",
    "Computational Genomics Unit, Center for Genomics and Data Science Research, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA",
    "Graduate Program in Bioinformatics and Systems Biology, University of California, San Diego, La Jolla, CA, USA",
    "Department of Biology, Johns Hopkins University, Baltimore, MD, USA",
    "Google LLC, Mountain View, CA, USA",
    "Beijing Institute of Genomics, Chinese Academy of Sciences, China National Center for Bioinformation, Beijing 100101, China",
    "Beijing Institute of Genomics, Chinese Academy of Sciences, and China National Center for Bioinformation, Beijing, 100101, China",
    "Core Unit Bioinformatics, Medical Faculty and University Hospital Düsseldorf, Heinrich-Heine-Universität Düsseldorf, Düsseldorf, Germany; Center for Digital Medicine, Heinrich-Heine-Universität Düsseldorf, Düsseldorf, Germany",
    "Center for Digital Medicine, Heinrich Heine University Dusseldorf, Germany",
    "Core Unit Bioinformatics, Medical Faculty and University Hospital Dusseldorf, Heinrich Heine University Dusseldorf, Germany",
    "Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA",
    "Broad Institute, Broad Clinical Labs, Burlington, MA, USA",
    "Vertebrate Genome Laboratory, the Rockefeller University, New York, NY, USA",
    "The Vertebrate Genome Laboratory, The Rockefeller University, NY, USA",
    "Bioinnovation and Genome Sciences, the Translational Genomics Research Institute (TGen), Phoenix, AZ 85004, USA",
    "Department of Genetics, Genomics and Informatics, University of Tennessee Health Science Center, Memphis, TN, USA",
    "Department of Computer Science, Johns Hopkins University, Baltimore, MD, USA; Department of Plant Sciences, University of Cambridge, Cambridge CB2 3EA, UK",
    "Department of Plant Sciences, University of Cambridge, Cambridge, UK, CB2 3EA",
    "Division of Animal Sciences, University of Missouri - Columbia, Columbia, MO, USA",
    "Division of Animal Sciences, University of Missouri, Columbia, MO, USA",
    "Oxford Nanopore Technologies, Oxford, UK",
    "Laboratory for Bioinformatics and Computational Biology, Faculty of Electrical Engineering and Computing, University of Zagreb, Zagreb, Croatia",
    "Coriell Institute for Medical Research, Camden, NJ, USA",
    "Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA; Genome Biology Unit, European Molecular Biology Laboratory (EMBL), 69117 Heidelberg, Germany",
    "Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA",
    "Genome Biology Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, 69117, Germany"
  ],
  "article_type": null,
  "arxiv": null,
  "author_total": 65,
  "authors": [
    {
      "affs": [
        0
      ],
      "name": "Nancy Fisher Hansen",
      "orcid": "0000-0002-0950-0699"
    },
    {
      "affs": [
        1
      ],
      "name": "Nathan J. Dwarshuis",
      "orcid": "0009-0001-9615-0243"
    },
    {
      "affs": [
        2,
        3
      ],
      "name": "Hyun Joo Ji",
      "orcid": "0009-0008-4360-5428"
    },
    {
      "affs": [
        0
      ],
      "name": "Arang Rhie",
      "orcid": "0000-0002-9809-8127"
    },
    {
      "affs": [
        4,
        5
      ],
      "name": "Hailey Loucks",
      "orcid": "0009-0000-6956-9922"
    },
    {
      "affs": [
        6
      ],
      "name": "Glennis A. Logsdon",
      "orcid": "0000-0003-2396-0656"
    },
    {
      "affs": [
        7,
        8
      ],
      "name": "Mitchell Robert Vollger",
      "orcid": "0000-0002-8651-1615"
    },
    {
      "affs": [
        9
      ],
      "name": "Jessica M. Storer",
      "orcid": "0000-0002-9619-5265"
    },
    {
      "affs": [
        0
      ],
      "name": "Juhyun Kim",
      "orcid": "0000-0001-5462-3391"
    },
    {
      "affs": [
        10
      ],
      "name": "Eleni Adam"
    },
    {
      "affs": [
        11,
        12,
        13
      ],
      "name": "Nicolas Altemose",
      "orcid": "0000-0002-7231-6026"
    },
    {
      "affs": [
        0
      ],
      "name": "Dmitry Antipov",
      "orcid": "0000-0002-6087-0660"
    },
    {
      "affs": [
        4,
        14
      ],
      "name": "Mobin Asri",
      "orcid": "0000-0002-7194-5138"
    },
    {
      "affs": [
        15
      ],
      "name": "Sofia N. Barreira",
      "orcid": "0000-0002-8450-135X"
    },
    {
      "affs": [
        7,
        8
      ],
      "name": "Stephanie C. Bohaczuk",
      "orcid": "0000-0001-8802-6579"
    },
    {
      "affs": [
        16
      ],
      "name": "Andrey V. Bzikadze",
      "orcid": "0000-0002-7928-7950"
    },
    {
      "affs": [
        17
      ],
      "name": "Sara A. Carioscia",
      "orcid": "0000-0002-0844-615X"
    },
    {
      "affs": [
        18
      ],
      "name": "Andrew W. Carroll",
      "orcid": "0000-0002-4824-6689"
    },
    {
      "affs": [
        2,
        3
      ],
      "name": "Kuan-Hao Chao",
      "orcid": "0000-0003-0099-0692"
    },
    {
      "affs": [
        19,
        20
      ],
      "name": "Yanan Chu",
      "orcid": "0000-0002-9349-4307"
    },
    {
      "affs": [
        3
      ],
      "name": "Arun Das",
      "orcid": "0000-0002-0332-1956"
    },
    {
      "affs": [
        21,
        22,
        23
      ],
      "name": "Peter Ebert",
      "orcid": "0000-0001-7441-532X"
    },
    {
      "affs": [
        24
      ],
      "name": "Adam C. English",
      "orcid": "0000-0003-2451-4375"
    },
    {
      "affs": [
        25
      ],
      "name": "Mark Fleharty",
      "orcid": "0000-0002-8141-8091"
    },
    {
      "affs": [
        25
      ],
      "name": "Laura E. Fleming"
    },
    {
      "affs": [
        26,
        27
      ],
      "name": "Giulio Formenti",
      "orcid": "0000-0002-7554-5991"
    },
    {
      "affs": [
        28,
        29
      ],
      "name": "Andrea Guarracino",
      "orcid": "0000-0001-9744-131X"
    },
    {
      "affs": [
        9
      ],
      "name": "Gabrielle A. Hartley",
      "orcid": "0000-0002-5672-2171"
    },
    {
      "affs": [
        30,
        3,
        31
      ],
      "name": "Katharine M. Jenike",
      "orcid": "0000-0002-7276-8110"
    },
    {
      "affs": [
        32,
        33
      ],
      "name": "Jenna Kalleberg",
      "orcid": "0000-0003-4505-8516"
    },
    {
      "affs": [
        19,
        20
      ],
      "name": "Yu Kang",
      "orcid": "0000-0002-0999-8802"
    },
    {
      "affs": [
        34
      ],
      "name": "Robert King"
    },
    {
      "affs": [
        35
      ],
      "name": "Josipa Lipovac",
      "orcid": "0009-0003-4943-5179"
    },
    {
      "affs": [
        4,
        5
      ],
      "name": "Mira Mastoras",
      "orcid": "0000-0001-6897-0116"
    },
    {
      "affs": [
        36
      ],
      "name": "Matthew W. Mitchell",
      "orcid": "0000-0002-6947-0495"
    },
    {
      "affs": [
        4,
        5
      ],
      "name": "Shloka Negi",
      "orcid": "0000-0002-9839-4030"
    },
    {
      "affs": [
        1
      ],
      "name": "Nathan D. Olson",
      "orcid": "0000-0003-2585-3037"
    },
    {
      "affs": [
        6
      ],
      "name": "Keisuke K. Oshima",
      "orcid": "0009-0002-2229-8998"
    },
    {
      "affs": [
        24
      ],
      "name": "Luis F. Paulin",
      "orcid": "0000-0003-2567-3773"
    },
    {
      "affs": [
        0
      ],
      "name": "Brandon D. Pickett",
      "orcid": "0000-0001-8235-4440"
    },
    {
      "affs": [
        37,
        38,
        39
      ],
      "name": "David Porubskỳ",
      "orcid": "0000-0001-8414-8966"
    },
    {
      "affs": [
        7,
        8
      ],
      "name": "Jane E. Ranchalis",
      "orcid": "0009-0004-1654-4114"
    },
    {
      "affs": [
        10
      ],
      "name": "Desh Ranjan",
      "orcid": "0000-0002-8298-7093"
    },
    {
      "name": "Mikko Rautiainen",
      "orcid": "0000-0003-2971-267X"
    },
    {
      "name": "Harold C. Riethman",
      "orcid": "0000-0003-4626-4733"
    },
    {
      "affs": [
        32,
        33
      ],
      "name": "Robert D. Schnabel",
      "orcid": "0000-0001-5018-7641"
    },
    {
      "name": "Fritz Joachim Sedlazeck",
      "orcid": "0000-0001-6040-2691"
    },
    {
      "affs": [
        18
      ],
      "name": "Kishwar Shafin",
      "orcid": "0000-0001-5252-3434"
    },
    {
      "affs": [
        35
      ],
      "name": "Mile Šikić",
      "orcid": "0000-0002-8370-0891"
    },
    {
      "affs": [
        0
      ],
      "name": "Steven J. Solar",
      "orcid": "0000-0003-3051-9009"
    },
    {
      "affs": [
        3,
        0
      ],
      "name": "Alexander P. Sweeten",
      "orcid": "0000-0002-5316-2973"
    },
    {
      "name": "Winston Timp",
      "orcid": "0000-0003-2083-6027"
    },
    {
      "affs": [
        1
      ],
      "name": "Justin Wagner",
      "orcid": "0009-0003-8903-0504"
    },
    {
      "affs": [
        38
      ],
      "name": "DongAhn Yoo",
      "orcid": "0000-0003-0033-3721"
    },
    {
      "name": "Ying Zhou",
      "orcid": "0000-0002-8107-3927"
    },
    {
      "name": "Erik P. Garrison",
      "orcid": "0000-0003-3821-631X"
    },
    {
      "affs": [
        38
      ],
      "name": "Evan E. Eichler",
      "orcid": "0000-0002-8246-4014"
    },
    {
      "affs": [
        3
      ],
      "name": "Michael C. Schatz",
      "orcid": "0000-0002-4118-4446"
    },
    {
      "affs": [
        38,
        8
      ],
      "name": "Andrew B. Stergachis",
      "orcid": "0000-0002-1299-3674"
    },
    {
      "affs": [
        9
      ],
      "name": "Rachel J. Waugh O'Neill",
      "orcid": "0000-0002-1525-6821"
    }
  ],
  "bibtex": "https://research.draconitic.com/paper/6pnvf4fec9fy6.bib",
  "cited_by": 65,
  "doi": "10.1016/j.cell.2026.06.016",
  "fulltext_url": null,
  "id": "6pnvf4fec9fy6",
  "issns": [
    "0092-8674",
    "1097-4172"
  ],
  "landing_url": "https://doi.org/10.1016/j.cell.2026.06.016",
  "language": "en",
  "licence": "CC-BY",
  "licence_label": "CC BY",
  "licence_source": "journal",
  "licence_url": "https://creativecommons.org/licenses/by/4.0/",
  "metadata_licence": null,
  "native_subjects": [
    [
      "openalex",
      "1312|Genomics and Phylogenetic Studies"
    ]
  ],
  "openalex": "W4414403753",
  "pdf_url": null,
  "pmcid": "PMC12458380",
  "pmid": "41000953",
  "published": "2026-08-01",
  "publisher": "Cell Press",
  "ris": "https://research.draconitic.com/paper/6pnvf4fec9fy6.ris",
  "sources": [
    {
      "first_seen": "2026-10-30T13:26:46Z",
      "native_id": "W4414403753",
      "source": "openalex",
      "url": "https://doi.org/10.1016/j.cell.2026.06.016"
    }
  ],
  "subjects": [
    {
      "field": "biochemistry",
      "origin": "openalex:1312|Genomics and Phylogenetic Studies",
      "subfield": "molecular-biology"
    }
  ],
  "title": "A complete diploid human genome benchmark for personalized genomics",
  "title_text": "A complete diploid human genome benchmark for personalized genomics",
  "type": "peer-reviewed",
  "updated_at": "2026-11-07T13:20:47Z",
  "url": "https://research.draconitic.com/paper/6pnvf4fec9fy6",
  "venue": "Cell",
  "versions": []
}