ArticleNature2022
Semi-automated assembly of high-quality diploid human reference genomes.
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Article in Nature, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 140 papers.
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140citing papers in PubMed
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Who cites it
140 citing papers in PubMed.
- Assembly-graph-assisted haplotype-resolved scaffolding of polyploid genomes.Nature plants · 2026Article
- An Icelandic pangenome reference.Nature · 2026Article
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- ChromoMapperWeb: evaluate genome alignments and track assembly steps within an interactive graphic environment.Nucleic acids research · 2026Article
- VCboost: reducing false positives in long-read variant calling for single-nucleotide polymorphism and indel detection in challenging genomic regions.Briefings in bioinformatics · 2026Article
- Article
- Near-perfect genome sequencing in medical genetics.Nature genetics · 2026Review
- The Vertebrate Genomes Project Phase I: A global reference genome resource.bioRxiv : the preprint server for biology · 2026Article
- MGA: a tool for haplotype-mixed assembly of long and accurate reads.Genome biology · 2026Article
- Accessing medically relevant complex regions with a pangenome graph of 20 near-complete Japanese haplotypes.Nature communications · 2026Article
- A new chromosome-level genome assembly for western painted turtle Chrysemys picta bellii, a model for extreme physiological adaptations.BMC genomics · 2026Article
- Evaluating genome assemblies with HMM-Flagger.bioRxiv : the preprint server for biology · 2026Article
- Time-Efficient and Informatic-Skill-Light Gap-Filling for Telomere-to-Telomere Genome Assembly.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Article
- Nallo: a Nextflow pipeline for comprehensive human long-read genome analysis.Bioinformatics (Oxford, England) · 2026Article
- Benchmarking long-read variant calling in diploid and polyploid genomes: insights from human and plants.BMC genomics · 2026Article
- Exploring potential transcription factors and their regulatory relationships based on asymmetric covariance natural vector encoding method and machine learning algorithms.Briefings in bioinformatics · 2026Article
- Benchmarking of Oxford Nanopore whole genome sequencing for germline variant and CpG methylation detection across Canada's national platform for genome sequencing and analysis.Frontiers in genetics · 2026Article
- Haplotype-Resolved Genomics Reveals Conserved Chromatin Architecture and Epigenetic Constraints of Human Neocentromeres.bioRxiv : the preprint server for biology · 2025Article
80 more citing papers are in PubMed but not listed here.
Corrections and comments
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Authors and funding
84 authors.
Erich D Jarvis *Vertebrate Genome Laboratory, The Rockefeller University, New York, NY, USA. ejarvis@rockefeller.edu.ORCID http://orcid.org/0000-0001-8931-5049
Giulio Formenti *Vertebrate Genome Laboratory, The Rockefeller University, New York, NY, USA. gformenti@rockefeller.edu.ORCID http://orcid.org/0000-0002-7554-5991
Arang RhieGenome Informatics Section, Computational and Statistical Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA.
Andrea GuarracinoGenomics Research Centre, Human Technopole, Viale Rita Levi-Montalcini, Milan, Italy.ORCID http://orcid.org/0000-0001-9744-131X
Chentao YangBGI-Shenzhen, Shenzhen, China.
Jonathan WoodTree of Life, Wellcome Sanger Institute, Cambridge, UK.ORCID http://orcid.org/0000-0002-7545-2162
Alan TraceyTree of Life, Wellcome Sanger Institute, Cambridge, UK.ORCID http://orcid.org/0000-0002-4805-9058
Francoise Thibaud-NissenNational Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA.ORCID http://orcid.org/0000-0003-4957-7807
Mitchell R VollgerDepartment of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA.ORCID http://orcid.org/0000-0002-8651-1615
David PorubskyDepartment of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA.ORCID http://orcid.org/0000-0001-8414-8966
Haoyu ChengDepartment of Data Sciences, Dana-Farber Cancer Institute, Boston, MA, USA.
Mobin AsriUC Santa Cruz Genomics Institute, University of California, Santa Cruz, CA, USA.
Glennis A LogsdonDepartment of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA.ORCID http://orcid.org/0000-0003-2396-0656
Paolo CarnevaliChan Zuckerberg Initiative, Redwood City, CA, USA.
Mark J P ChaissonQuantitative and Computational Biology, University of Southern California, Los Angeles, CA, USA.ORCID http://orcid.org/0000-0001-5395-1457
Chen-Shan ChinFoundation for Biological Data Science, Belmont, CA, USA.
Sarah CodyMcDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO, USA.
Joanna CollinsTree of Life, Wellcome Sanger Institute, Cambridge, UK.
Peter EbertInstitute for Medical Biometry and Bioinformatics, Medical Faculty, Heinrich Heine University, Düsseldorf, Germany.ORCID http://orcid.org/0000-0001-7441-532X
Merly EscalonaDepartment of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, CA, USA.ORCID http://orcid.org/0000-0003-0213-4777
Olivier FedrigoVertebrate Genome Laboratory, The Rockefeller University, New York, NY, USA.ORCID http://orcid.org/0000-0002-6450-7551
Robert S FultonMcDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO, USA.
Lucinda L FultonMcDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO, USA.
Shilpa GargDepartment of Biology, University of Copenhagen, Copenhagen, Denmark.
Jennifer L GertonStowers Institute for Medical Research, Kansas City, MO, USA.ORCID http://orcid.org/0000-0003-0743-3637
Jay GhuryeDovetail Genomics, Scotts Valley, CA, USA.
Anastasiya GranatIllumina, Inc., San Diego, CA, USA.
Richard E GreenUC Santa Cruz Genomics Institute, University of California, Santa Cruz, CA, USA.ORCID http://orcid.org/0000-0003-0516-5827
William HarveyDepartment of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA.
Patrick HasenfeldEuropean Molecular Biology Laboratory, Genome Biology Unit, Heidelberg, Germany.ORCID http://orcid.org/0000-0003-2319-2482
Alex HastieBionano Genomics, San Diego, CA, USA.
Marina HauknessUC Santa Cruz Genomics Institute, University of California, Santa Cruz, CA, USA.ORCID http://orcid.org/0000-0001-9991-8089
Erich B JaegerIllumina, Inc., San Diego, CA, USA.
Miten JainUC Santa Cruz Genomics Institute, University of California, Santa Cruz, CA, USA.
Melanie KirscheDepartment of Computer Science, Johns Hopkins University, Baltimore, MD, USA.
Mikhail KolmogorovDepartment of Computer Science and Engineering, University of California San Diego, La Jolla, CA, USA.ORCID http://orcid.org/0000-0002-5489-9045
Jan O KorbelEuropean Molecular Biology Laboratory, Genome Biology Unit, Heidelberg, Germany.ORCID http://orcid.org/0000-0002-2798-3794
Sergey KorenGenome Informatics Section, Computational and Statistical Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA.ORCID http://orcid.org/0000-0002-1472-8962
Jonas KorlachPacific Biosciences, Menlo Park, CA, USA.ORCID http://orcid.org/0000-0003-3047-4250
Joyce LeeBionano Genomics, San Diego, CA, USA.ORCID http://orcid.org/0000-0002-3492-1102
Daofeng LiDepartment of Genetics, Washington University School of Medicine, St. Louis, MO, USA.ORCID http://orcid.org/0000-0001-7492-3703
Tina LindsayMcDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO, USA.
Julian LucasUC Santa Cruz Genomics Institute, University of California, Santa Cruz, CA, USA.
Feng LuoSchool of Computing, Clemson University, Clemson, SC, USA.ORCID http://orcid.org/0000-0002-4813-2403
Tobias MarschallInstitute for Medical Biometry and Bioinformatics, Medical Faculty, Heinrich Heine University, Düsseldorf, Germany.ORCID http://orcid.org/0000-0002-9376-1030
Matthew W MitchellCoriell Institute for Medical Research, Camden, NJ, USA.
Jennifer McDanielMaterial Measurement Laboratory, National Institute of Standards and Technology, Gaithersburg, MD, USA.ORCID http://orcid.org/0000-0003-1987-0914
Fan NieHunan Provincial Key Lab on Bioinformatics, School of Computer Science and Engineering, Central South University, Changsha, China.
Hugh E OlsenUC Santa Cruz Genomics Institute, University of California, Santa Cruz, CA, USA.
Nathan D OlsonMaterial Measurement Laboratory, National Institute of Standards and Technology, Gaithersburg, MD, USA.ORCID http://orcid.org/0000-0003-2585-3037
Trevor PesoutUC Santa Cruz Genomics Institute, University of California, Santa Cruz, CA, USA.
Tamara PotapovaStowers Institute for Medical Research, Kansas City, MO, USA.
Daniela PuiuDepartment of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, USA.
Allison RegierDNAnexus, Mountain View, CA, USA.
Jue RuanAgricultural Genomics Institute, Chinese Academy of Agricultural Sciences, Shenzhen, China.
Steven L SalzbergDepartment of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, USA.
Ashley D SandersBerlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany.
Michael C SchatzDepartment of Computer Science, Johns Hopkins University, Baltimore, MD, USA.
Anthony SchmittArima Genomics, San Diego, CA, USA.
Valerie A SchneiderNational Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA.
Siddarth SelvarajArima Genomics, San Diego, CA, USA.
Kishwar ShafinUC Santa Cruz Genomics Institute, University of California, Santa Cruz, CA, USA.ORCID http://orcid.org/0000-0001-5252-3434
Alaina ShumateDepartment of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, USA.
Nathan O StitzielMcDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO, USA.ORCID http://orcid.org/0000-0002-4963-8211
Catherine StoberEuropean Molecular Biology Laboratory, Genome Biology Unit, Heidelberg, Germany.
James TorranceTree of Life, Wellcome Sanger Institute, Cambridge, UK.
Justin WagnerMaterial Measurement Laboratory, National Institute of Standards and Technology, Gaithersburg, MD, USA.
Jianxin WangHunan Provincial Key Lab on Bioinformatics, School of Computer Science and Engineering, Central South University, Changsha, China.ORCID http://orcid.org/0000-0003-1516-0480
Aaron WengerPacific Biosciences, Menlo Park, CA, USA.
Chuanle XiaoState Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou, China.ORCID http://orcid.org/0000-0002-4680-0682
Aleksey V ZiminDepartment of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, USA.
Guojie ZhangCenter for Evolutionary & Organismal Biology, Zhejiang University School of Medicine, Hangzhou, China.ORCID http://orcid.org/0000-0001-6860-1521
Ting WangMcDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO, USA.ORCID http://orcid.org/0000-0002-6800-242X
Heng LiDepartment of Data Sciences, Dana-Farber Cancer Institute, Boston, MA, USA.ORCID http://orcid.org/0000-0003-4874-2874
Erik GarrisonDepartment of Genetics, Genomics and Informatics, University of Tennessee Health Science Center, Memphis, TN, USA.
David HausslerHoward Hughes Medical Institute, Chevy Chase, MD, USA.ORCID http://orcid.org/0000-0003-1533-4575
Ira HallYale School of Medicine, New Haven, CT, USA.
Justin M ZookMaterial Measurement Laboratory, National Institute of Standards and Technology, Gaithersburg, MD, USA.
Evan E EichlerHoward Hughes Medical Institute, Chevy Chase, MD, USA.ORCID http://orcid.org/0000-0002-8246-4014
Adam M PhillippyGenome Informatics Section, Computational and Statistical Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA.ORCID http://orcid.org/0000-0003-2983-8934
Benedict PatenUC Santa Cruz Genomics Institute, University of California, Santa Cruz, CA, USA.
Kerstin HoweTree of Life, Wellcome Sanger Institute, Cambridge, UK. kj2@sanger.ac.uk.ORCID http://orcid.org/0000-0003-2237-513X
Karen H MigaUC Santa Cruz Genomics Institute, University of California, Santa Cruz, CA, USA. khmiga@ucsc.edu.
Human Pangenome Reference Consortium
Funding
ELSI Administrative Supplement - Center for Human Reference Genome DiversityU01HG010971 · NHGRI · UNIVERSITY OF CALIFORNIA SANTA CRUZ · PI EICHLER, EVAN, JARVIS, ERICH D · 2019 to 2023
$18.4MSequence and Assembly of Segmental DuplicationsR01HG002385 · NHGRI · UNIVERSITY OF WASHINGTON · PI Evan Eichler · 2001 to 2026
$13.3MComputational Methods for Genome Assembly, Transcript Assembly, and Variant DiscoveryR01HG006677 · NHGRI · JOHNS HOPKINS UNIVERSITY · PI SALZBERG, STEVEN L. · 2011 to 2025
$10.7MSequence-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
$4.5MAdvanced computational methods in analyzing high-throughput sequencing dataR01HG010040 · NHGRI · DANA-FARBER CANCER INST · PI Heng Li · 2018 to 2026
$3.7MThe construction and utility of reference pan-genome graphsU01HG010961 · NHGRI · DANA-FARBER CANCER INST · PI LI, HENG, PATEN, BENEDICT · 2020 to 2023
$3.2MIntegrative genomic and epigenomic analysis of cancer using long read sequencingU01CA253481 · NCI · JOHNS HOPKINS UNIVERSITY · PI SCHATZ, MICHAEL · 2021 to 2023
$1.1MDirect whole-genome haplotype-resolved assembly using sequence graphsK99HG010906 · NHGRI · DANA-FARBER CANCER INST · PI GARG, SHILPA · 2019 to 2020
$167kHoward Hughes Medical InstituteNCI NIH HHS U01 CA253481NHGRI NIH HHS K99 HG010906NHGRI NIH HHS R01 HG002385NHGRI NIH HHS R01 HG010169NHGRI NIH HHS R01 HG011274NHGRI NIH HHS U01 HG010971
Abstract
The current human reference genome, GRCh38, represents over 20 years of effort to generate a high-quality assembly, which has benefitted society
Indexed as
Chromosome MappingDiploidyGenome, HumanGenomicsChromosomes, HumanGenetic VariationHaplotypesHigh-Throughput Nucleotide SequencingHumansReference StandardsSequence Analysis, DNA
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