ArticleCell2026
A complete diploid human genome benchmark for personalized genomics.
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Article in Cell, 2026. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 45 papers.
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45citing papers in PubMed
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Who cites it
45 citing papers in PubMed.
- SVPG: a pangenome-based structural variant detection approach and rapid augmentation of pangenome graphs with new samples.Nature methods · 2026Article
- dicast: a machine learning method for accurate structural variant detection from short-read sequencing data.Genome biology · 2026Article
- Defining and cataloging variants in pangenome graphs.Cell genomics · 2026Article
- Structural Variant benchmarking frameworks: Parameterization, matching logic, and evaluation assumptions presented through HG002 and NA12878.PLoS computational biology · 2026Article
- Haplotype-resolved DiMeLo-seq maps centromeric chromatin in a complete diploid human genome.Cell genomics · 2026Article
- Finishing a complete giraffe genome from telomere to telomere with Verkko-Fillet.Cell genomics · 2026Article
- Automatic generation of model sequences for complex regions in assembly graphs with TTT.Cell genomics · 2026Article
- Article
- DOM: Dual Optical Mapping Integrating Sequence-Specific Barcodes and A/T Density Profiles.Small methods · 2026Article
- Leveraging ONT move table values for signal aware variant calling.Bioinformatics (Oxford, England) · 2026Article
- Article
- HPRC2: A human pangenome reference with near-complete coverage of common genetic variation.bioRxiv : the preprint server for biology · 2026Article
- Direct detection of alternative DNA conformations with long-read sequencing and machine learning approaches.bioRxiv : the preprint server for biology · 2026Article
- Navigating the pangenome coordinate system with Shredtools.bioRxiv : the preprint server for biology · 2026Article
- Article
- Short-Read Sequencing Benchmarking with Donor-Specific Assemblies.bioRxiv : the preprint server for biology · 2026Article
- The Vertebrate Genomes Project Phase I: A global reference genome resource.bioRxiv : the preprint server for biology · 2026Article
- Aardvark: sifting through differences in a mound of variants.Genome biology · 2026Article
- Germline sequence variation within the ribosomal DNA is associated with human complex traits.Cell genomics · 2026Article
- Population-scale Y chromosome assemblies reveal recurrent remodeling within constrained architectures.bioRxiv : the preprint server for biology · 2026Article
Corrections and comments
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Authors and funding
65 authors.
Nancy F HansenGenome Informatics Section, Center for Genomics and Data Science Research, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA.
Nathan DwarshuisMaterial Measurement Laboratory, National Institute of Standards and Technology, Gaithersburg, MD, USA.
Hyun Joo JiDepartment of Computer Science, Johns Hopkins University, Baltimore, MD, USA; Center for Computational Biology, Johns Hopkins University, Baltimore, MD, USA.
Arang RhieGenome Informatics Section, Center for Genomics and Data Science Research, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA.
Hailey LoucksUniversity of California, Santa Cruz Genomics Institute, University of California, Santa Cruz, Santa Cruz, CA, USA.
Glennis A LogsdonDepartment of Genetics, Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
Mitchell R VollgerDivision of Medical Genetics, Department of Medicine, University of Washington School of Medicine, Seattle, WA, USA.
Jessica M StorerInstitute for Systems Genomics, University of Connecticut, Storrs, CT, USA.
Juhyun KimGenome Informatics Section, Center for Genomics and Data Science Research, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA.
Eleni AdamDepartment of Computer Science, Old Dominion University, Norfolk, VA, USA.
Nicolas AltemoseDepartment of Genetics, School of Medicine, Stanford University, Palo Alto, CA, USA; Chan Zuckerberg Biohub, San Francisco, CA, USA.
Dmitry AntipovGenome Informatics Section, Center for Genomics and Data Science Research, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA.
Mobin AsriUniversity of California, Santa Cruz Genomics Institute, University of California, Santa Cruz, Santa Cruz, CA, USA.
Sofia BarreiraComputational Genomics Unit, Center for Genomics and Data Science Research, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA.
Stephanie C BohaczukDivision of Medical Genetics, Department of Medicine, University of Washington School of Medicine, Seattle, WA, USA.
Andrey V BzikadzeGraduate Program in Bioinformatics and Systems Biology, University of California, San Diego, La Jolla, CA, USA.
Sara A CariosciaDepartment of Biology, Johns Hopkins University, Baltimore, MD, USA.
Andrew CarrollGoogle LLC, Mountain View, CA, USA.
Kuan-Hao ChaoDepartment of Computer Science, Johns Hopkins University, Baltimore, MD, USA; Center for Computational Biology, Johns Hopkins University, Baltimore, MD, USA.
Yanan ChuBeijing Institute of Genomics, Chinese Academy of Sciences, China National Center for Bioinformation, Beijing 100101, China.
Arun DasDepartment of Computer Science, Johns Hopkins University, Baltimore, MD, USA.
Peter EbertCore Unit Bioinformatics, Medical Faculty and University Hospital Düsseldorf, Heinrich-Heine-Universität Düsseldorf, Düsseldorf, Germany; Center for Digital Medicine, Heinrich-Heine-Universität Düsseldorf, Düsseldorf, Germany.
Adam EnglishHuman Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA.
Mark FlehartyBroad Institute, Broad Clinical Labs, Burlington, MA, USA.
Laura E FlemingBroad Institute, Broad Clinical Labs, Burlington, MA, USA.
Giulio FormentiVertebrate Genome Laboratory, the Rockefeller University, New York, NY, USA.
Andrea GuarracinoBioinnovation and Genome Sciences, the Translational Genomics Research Institute (TGen), Phoenix, AZ 85004, USA.
Gabrielle A HartleyInstitute for Systems Genomics, University of Connecticut, Storrs, CT, USA.
Katharine JenikeDepartment of Computer Science, Johns Hopkins University, Baltimore, MD, USA; Department of Plant Sciences, University of Cambridge, Cambridge CB2 3EA, UK.
Jenna KallebergDivision of Animal Sciences, University of Missouri - Columbia, Columbia, MO, USA.
Yu KangBeijing Institute of Genomics, Chinese Academy of Sciences, China National Center for Bioinformation, Beijing 100101, China.
Robert KingOxford Nanopore Technologies, Oxford, UK.
Josipa LipovacLaboratory for Bioinformatics and Computational Biology, Faculty of Electrical Engineering and Computing, University of Zagreb, Zagreb, Croatia.
Mira MastorasUniversity of California, Santa Cruz Genomics Institute, University of California, Santa Cruz, Santa Cruz, CA, USA.
Matthew W MitchellCoriell Institute for Medical Research, Camden, NJ, USA.
Shloka NegiUniversity of California, Santa Cruz Genomics Institute, University of California, Santa Cruz, Santa Cruz, CA, USA.
Nathan D OlsonMaterial Measurement Laboratory, National Institute of Standards and Technology, Gaithersburg, MD, USA.
Keisuke K OshimaDepartment of Genetics, Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
Luis F PaulinHuman Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA.
Brandon D PickettGenome Informatics Section, Center for Genomics and Data Science Research, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA.
David PorubskyDepartment of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA; Genome Biology Unit, European Molecular Biology Laboratory (EMBL), 69117 Heidelberg, Germany.
Jane RanchalisDivision of Medical Genetics, Department of Medicine, University of Washington School of Medicine, Seattle, WA, USA.
Desh RanjanDepartment of Computer Science, Old Dominion University, Norfolk, VA, USA.
Mikko RautiainenInstitute for Molecular Medicine Finland, Helsinki Institute of Life Science, University of Helsinki, Helsinki, Finland.
Harold RiethmanSchool of Medical Diagnostic & Translational Sciences, Old Dominion University, Norfolk, VA, USA.
Robert D SchnabelDivision of Animal Sciences, University of Missouri - Columbia, Columbia, MO, USA.
Fritz J SedlazeckHuman Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA; Department of Computer Science, Rice University, Houston, TX, USA.
Kishwar ShafinGoogle LLC, Mountain View, CA, USA.
Mile SikicLaboratory for Bioinformatics and Computational Biology, Faculty of Electrical Engineering and Computing, University of Zagreb, Zagreb, Croatia; Genome Institute of Singapore, A(∗)STAR, Singapore, Republic of Singapore.
Steven J SolarGenome Informatics Section, Center for Genomics and Data Science Research, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA.
Alexander P SweetenGenome Informatics Section, Center for Genomics and Data Science Research, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA; Department of Computer Science, Johns Hopkins University, Baltimore, MD, USA.
Winston TimpDepartment of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, USA.
Justin WagnerMaterial Measurement Laboratory, National Institute of Standards and Technology, Gaithersburg, MD, USA.
DongAhn YooDepartment of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA.
Ying ZhouDepartment of Data Science, Dana-Farber Cancer Institute, Boston, MA, USA.
Erik GarrisonDepartment of Genetics, Genomics, and Informatics, University of Tennessee Health Science Center, Memphis, TN, USA.
Evan E EichlerDepartment of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA; Howard Hughes Medical Institute, University of Washington, Seattle, WA, USA.
Michael C SchatzDepartment of Computer Science, Johns Hopkins University, Baltimore, MD, USA.
Andrew B StergachisDivision of Medical Genetics, Department of Medicine, University of Washington School of Medicine, Seattle, WA, USA; Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA; Brotman Baty Institute for Precision Medicine, Seattle, WA, USA.
Rachel J O'NeillInstitute for Systems Genomics, University of Connecticut, Storrs, CT, USA; Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT, USA; Department of Genome Sciences, UConn Health, Farmington, CT, USA.
Karen H MigaUniversity of California, Santa Cruz Genomics Institute, University of California, Santa Cruz, Santa Cruz, CA, USA.
Steven L SalzbergDepartment of Computer Science, Johns Hopkins University, Baltimore, MD, USA; Center for Computational Biology, Johns Hopkins University, Baltimore, MD, USA; Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, USA; Department of Biostatistics, Johns Hopkins University, Baltimore, MD, USA.
Sergey KorenGenome Informatics Section, Center for Genomics and Data Science Research, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA.
Justin M ZookMaterial Measurement Laboratory, National Institute of Standards and Technology, Gaithersburg, MD, USA. Electronic address: justin.zook@nist.gov.
Adam M PhillippyGenome Informatics Section, Center for Genomics and Data Science Research, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA; Department of Computer Science, Johns Hopkins University, Baltimore, MD, USA; Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, USA; Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA. Electronic address: aphillippy@jhu.edu.
Funding
Implementing the Genomic Data Science Analysis, Visualization, and Informatics Lab-space (AnVIL)U24HG010263 · NHGRI · JOHNS HOPKINS UNIVERSITY · PI Enis Afgan, VINCENT JAMES CAREY · 2018 to 2026
$23.8MSingle-molecule sequence assembly and analysisZIAHG200398 · NHGRI · NATIONAL HUMAN GENOME RESEARCH INSTITUTE · PI PHILLIPPY, ADAM · 2016 to 2025
$15.9MSomatic Mosaicism across Human Tissues Program: Genome Characterization Centers (GCC SMaHT)UM1DA058220 · NIDA · SEATTLE CHILDREN'S HOSPITAL · PI JAMES T BENNETT, Evan Eichler · 2023 to 2026
$15.2MComprehensive Somatic Variant Characterization at the HGSCUM1DA058229 · NIDA · BAYLOR COLLEGE OF MEDICINE · PI Harsha Vardhan Doddapaneni, RICHARD A GIBBS · 2023 to 2026
$15.0MFrequency of variants of unknown significance by ancestry groups in the All of Us Research Program cohortU01HG011758 · NHGRI · BAYLOR COLLEGE OF MEDICINE · PI RICHARD A GIBBS, JAMES R. LUPSKI · 2021 to 2026
$13.8MComputational Methods for Genome Assembly, Transcript Assembly, and Variant DiscoveryR01HG006677 · NHGRI · JOHNS HOPKINS UNIVERSITY · PI SALZBERG, STEVEN L. · 2011 to 2025
$10.7MCenter for Human Genome Reference DiversityUM1HG010971 · NHGRI · UNIVERSITY OF CALIFORNIA SANTA CRUZ · PI Robert Mullan Cook-Deegan, Evan Eichler · 2024 to 2026
$8.6MMedical Genetics Training GrantT32GM007454 · NIGMS · UNIVERSITY OF WASHINGTON · PI Gail Pairitz Jarvik, Andrew Ben Stergachis · 1985 to 2026
$6.9MSequence-resolved structural variation of human genomesR01HG010169 · NHGRI · UNIVERSITY OF WASHINGTON · PI Evan Eichler · 2018 to 2026
$4.5MTelomere-to-telomere assemblies of human genomesR01HG011274 · NHGRI · UNIVERSITY OF CALIFORNIA SANTA CRUZ · PI Karen Hayden Miga · 2020 to 2026
$4.5MComputational Methods for Microbial and Microbiome Sequence AnalysisR35GM130151 · NIGMS · JOHNS HOPKINS UNIVERSITY · PI Steven L. Salzberg · 2019 to 2026
$2.9MInvestigating the contribution of non-coding genetic variation to rare disordersDP5OD029630 · OD · UNIVERSITY OF WASHINGTON · PI STERGACHIS, ANDREW BEN · 2020 to 2024
$1.9MIntramural NIH HHS ZIA HG200398Intramural NIST DOC 9999-NISTNHGRI NIH HHS R01 HG006677NHGRI NIH HHS R01 HG010169NHGRI NIH HHS R01 HG011274NHGRI NIH HHS U01 HG011758NHGRI NIH HHS U01 HG013744NHGRI NIH HHS U24 HG010263NHGRI NIH HHS UM1 HG010971NIDA NIH HHS UM1 DA058220NIDA NIH HHS UM1 DA058229NIGMS NIH HHS K99 GM155552NIGMS NIH HHS R00 GM147352NIGMS NIH HHS R35 GM130151NIGMS NIH HHS R35 GM156470NIGMS NIH HHS T32 GM007454NIH HHS DP5 OD029630NINDS NIH HHS UG3 NS132105
Abstract
Human genome sequencing typically relies on mapping reads to a reference genome to call variants, but this approach introduces technical biases, excluding duplicated and structurally polymorphic regions of the genome. To overcome this, we present a telomere-to-telomere genome benchmark with near-perfect accuracy across 99.4% of the diploid HG002 genome. This benchmark adds 701.4 Mb of autosomal sequence and both sex chromosomes (216.8 Mb), which were absent from prior benchmarks. We annotated genes and repeats on both haplotypes, including 19,956 protein-coding genes on the maternal haplotype and 19,190 on the paternal haplotype, and developed new methods to measure the accuracy of reads, phased variant call sets, and assemblies against a diploid reference. Genome-wide analyses show that de novo assembly resolves 2%-7% more sequence and outperforms variant calling accuracy by an order of magnitude, expanding the reach of genomic medicine to the entire genome and enabling a new era of personalized genomics.
Indexed as
DiploidyGenome, HumanGenomicsHaplotypesHumansPrecision MedicineSequence Analysis, DNATelomerebenchmarkingdiploidgenome annotationgenome assemblygenome sequencinggenomicshaplotypestelomere-to-telomere
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