Accurate circular consensus long-read sequencing improves variant detection and assembly of a human genome View Full Text


Ontology type: schema:ScholarlyArticle      Open Access: True


Article Info

DATE

2019-08-12

AUTHORS

Aaron M. Wenger, Paul Peluso, William J. Rowell, Pi-Chuan Chang, Richard J. Hall, Gregory T. Concepcion, Jana Ebler, Arkarachai Fungtammasan, Alexey Kolesnikov, Nathan D. Olson, Armin Töpfer, Michael Alonge, Medhat Mahmoud, Yufeng Qian, Chen-Shan Chin, Adam M. Phillippy, Michael C. Schatz, Gene Myers, Mark A. DePristo, Jue Ruan, Tobias Marschall, Fritz J. Sedlazeck, Justin M. Zook, Heng Li, Sergey Koren, Andrew Carroll, David R. Rank, Michael W. Hunkapiller

ABSTRACT

The DNA sequencing technologies in use today produce either highly accurate short reads or less-accurate long reads. We report the optimization of circular consensus sequencing (CCS) to improve the accuracy of single-molecule real-time (SMRT) sequencing (PacBio) and generate highly accurate (99.8%) long high-fidelity (HiFi) reads with an average length of 13.5 kilobases (kb). We applied our approach to sequence the well-characterized human HG002/NA24385 genome and obtained precision and recall rates of at least 99.91% for single-nucleotide variants (SNVs), 95.98% for insertions and deletions <50 bp (indels) and 95.99% for structural variants. Our CCS method matches or exceeds the ability of short-read sequencing to detect small variants and structural variants. We estimate that 2,434 discordances are correctable mistakes in the ‘genome in a bottle’ (GIAB) benchmark set. Nearly all (99.64%) variants can be phased into haplotypes, further improving variant detection. De novo genome assembly using CCS reads alone produced a contiguous and accurate genome with a contig N50 of >15 megabases (Mb) and concordance of 99.997%, substantially outperforming assembly with less-accurate long reads. More... »

PAGES

1155-1162

References to SciGraph publications

  • 2001-02-15. Initial sequencing and analysis of the human genome in NATURE
  • 2019-12-09. Fast and accurate long-read assembly with wtdbg2 in NATURE METHODS
  • 2013-05-05. Nonhybrid, finished microbial genome assemblies from long-read SMRT sequencing data in NATURE METHODS
  • 2019-04-01. An open resource for accurately benchmarking small variant and reference calls in NATURE BIOTECHNOLOGY
  • 2016-06-07. Extensive sequencing of seven human genomes to characterize benchmark reference materials in SCIENTIFIC DATA
  • 2018-03-27. A Sequel to Sanger: amplicon sequencing that scales in BMC GENOMICS
  • 2017-01-24. Transient structural variations have strong effects on quantitative traits and reproductive isolation in fission yeast in NATURE COMMUNICATIONS
  • 2008-11. Accurate whole human genome sequencing using reversible terminator chemistry in NATURE
  • 2014-11-10. Resolving the complexity of the human genome using single-molecule sequencing in NATURE
  • 2019-03-01. A multi-task convolutional deep neural network for variant calling in single molecule sequencing in NATURE COMMUNICATIONS
  • 2011-07-20. An integrated semiconductor device enabling non-optical genome sequencing in NATURE
  • <error retrieving object. in <ERROR RETRIEVING OBJECT
  • 2018-12-17. Long-read sequence and assembly of segmental duplications in NATURE METHODS
  • 2014. Efficient Local Alignment Discovery amongst Noisy Long Reads in ALGORITHMS IN BIOINFORMATICS
  • 2018-03-29. Piercing the dark matter: bioinformatics of long-range sequencing and mapping in NATURE REVIEWS GENETICS
  • 2018-10-22. De novo assembly of haplotype-resolved genomes with trio binning in NATURE BIOTECHNOLOGY
  • 2018-09-24. A universal SNP and small-indel variant caller using deep neural networks in NATURE BIOTECHNOLOGY
  • 2018-07-16. A synthetic-diploid benchmark for accurate variant-calling evaluation in NATURE METHODS
  • 2016-10-05. De novo assembly and phasing of a Korean human genome in NATURE
  • 2019-04-16. Multi-platform discovery of haplotype-resolved structural variation in human genomes in NATURE COMMUNICATIONS
  • 2017-11-06. Mapping and phasing of structural variation in patient genomes using nanopore sequencing in NATURE COMMUNICATIONS
  • 2016-10-17. Phased diploid genome assembly with single-molecule real-time sequencing in NATURE METHODS
  • 1986-06. Fluorescence detection in automated DNA sequence analysis in NATURE
  • 2002-12. Initial sequencing and comparative analysis of the mouse genome in NATURE
  • 2019-03-11. Best practices for benchmarking germline small-variant calls in human genomes in NATURE BIOTECHNOLOGY
  • 2000-12. Analysis of the genome sequence of the flowering plant Arabidopsis thaliana in NATURE
  • 2018-01-29. Nanopore sequencing and assembly of a human genome with ultra-long reads in NATURE BIOTECHNOLOGY
  • 2018-04-30. Accurate detection of complex structural variations using single-molecule sequencing in NATURE METHODS
  • 2016-05-26. Navigating highly homologous genes in a molecular diagnostic setting: a resource for clinical next-generation sequencing in GENETICS IN MEDICINE
  • 2018-06-02. High-Resolution Full-Length HLA Typing Method Using Third Generation (Pac-Bio SMRT) Sequencing Technology in HLA TYPING
  • 2011-04-10. A framework for variation discovery and genotyping using next-generation DNA sequencing data in NATURE GENETICS
  • Identifiers

    URI

    http://scigraph.springernature.com/pub.10.1038/s41587-019-0217-9

    DOI

    http://dx.doi.org/10.1038/s41587-019-0217-9

    DIMENSIONS

    https://app.dimensions.ai/details/publication/pub.1120285368

    PUBMED

    https://www.ncbi.nlm.nih.gov/pubmed/31406327


    Indexing Status Check whether this publication has been indexed by Scopus and Web Of Science using the SN Indexing Status Tool
    Incoming Citations Browse incoming citations for this publication using opencitations.net

    JSON-LD is the canonical representation for SciGraph data.

    TIP: You can open this SciGraph record using an external JSON-LD service: JSON-LD Playground Google SDTT

    [
      {
        "@context": "https://springernature.github.io/scigraph/jsonld/sgcontext.json", 
        "about": [
          {
            "id": "http://purl.org/au-research/vocabulary/anzsrc-for/2008/06", 
            "inDefinedTermSet": "http://purl.org/au-research/vocabulary/anzsrc-for/2008/", 
            "name": "Biological Sciences", 
            "type": "DefinedTerm"
          }, 
          {
            "id": "http://purl.org/au-research/vocabulary/anzsrc-for/2008/0604", 
            "inDefinedTermSet": "http://purl.org/au-research/vocabulary/anzsrc-for/2008/", 
            "name": "Genetics", 
            "type": "DefinedTerm"
          }, 
          {
            "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
            "name": "Base Sequence", 
            "type": "DefinedTerm"
          }, 
          {
            "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
            "name": "DNA, Circular", 
            "type": "DefinedTerm"
          }, 
          {
            "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
            "name": "Genetic Variation", 
            "type": "DefinedTerm"
          }, 
          {
            "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
            "name": "Genome, Human", 
            "type": "DefinedTerm"
          }, 
          {
            "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
            "name": "Haplotypes", 
            "type": "DefinedTerm"
          }, 
          {
            "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
            "name": "High-Throughput Nucleotide Sequencing", 
            "type": "DefinedTerm"
          }, 
          {
            "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
            "name": "Humans", 
            "type": "DefinedTerm"
          }, 
          {
            "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
            "name": "Sequence Analysis, DNA", 
            "type": "DefinedTerm"
          }
        ], 
        "author": [
          {
            "affiliation": {
              "alternateName": "Pacific Biosciences, Menlo Park, CA, USA", 
              "id": "http://www.grid.ac/institutes/grid.423340.2", 
              "name": [
                "Pacific Biosciences, Menlo Park, CA, USA"
              ], 
              "type": "Organization"
            }, 
            "familyName": "Wenger", 
            "givenName": "Aaron M.", 
            "id": "sg:person.012106407613.52", 
            "sameAs": [
              "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.012106407613.52"
            ], 
            "type": "Person"
          }, 
          {
            "affiliation": {
              "alternateName": "Pacific Biosciences, Menlo Park, CA, USA", 
              "id": "http://www.grid.ac/institutes/grid.423340.2", 
              "name": [
                "Pacific Biosciences, Menlo Park, CA, USA"
              ], 
              "type": "Organization"
            }, 
            "familyName": "Peluso", 
            "givenName": "Paul", 
            "id": "sg:person.01145166025.52", 
            "sameAs": [
              "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01145166025.52"
            ], 
            "type": "Person"
          }, 
          {
            "affiliation": {
              "alternateName": "Pacific Biosciences, Menlo Park, CA, USA", 
              "id": "http://www.grid.ac/institutes/grid.423340.2", 
              "name": [
                "Pacific Biosciences, Menlo Park, CA, USA"
              ], 
              "type": "Organization"
            }, 
            "familyName": "Rowell", 
            "givenName": "William J.", 
            "id": "sg:person.012465005413.81", 
            "sameAs": [
              "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.012465005413.81"
            ], 
            "type": "Person"
          }, 
          {
            "affiliation": {
              "alternateName": "Google Inc., Mountain View, CA, USA", 
              "id": "http://www.grid.ac/institutes/grid.420451.6", 
              "name": [
                "Google Inc., Mountain View, CA, USA"
              ], 
              "type": "Organization"
            }, 
            "familyName": "Chang", 
            "givenName": "Pi-Chuan", 
            "id": "sg:person.012731257213.44", 
            "sameAs": [
              "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.012731257213.44"
            ], 
            "type": "Person"
          }, 
          {
            "affiliation": {
              "alternateName": "Pacific Biosciences, Menlo Park, CA, USA", 
              "id": "http://www.grid.ac/institutes/grid.423340.2", 
              "name": [
                "Pacific Biosciences, Menlo Park, CA, USA"
              ], 
              "type": "Organization"
            }, 
            "familyName": "Hall", 
            "givenName": "Richard J.", 
            "type": "Person"
          }, 
          {
            "affiliation": {
              "alternateName": "Pacific Biosciences, Menlo Park, CA, USA", 
              "id": "http://www.grid.ac/institutes/grid.423340.2", 
              "name": [
                "Pacific Biosciences, Menlo Park, CA, USA"
              ], 
              "type": "Organization"
            }, 
            "familyName": "Concepcion", 
            "givenName": "Gregory T.", 
            "id": "sg:person.0655453307.39", 
            "sameAs": [
              "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0655453307.39"
            ], 
            "type": "Person"
          }, 
          {
            "affiliation": {
              "alternateName": "Graduate School of Computer Science, Saarland University, Saarbr\u00fccken, Germany", 
              "id": "http://www.grid.ac/institutes/grid.11749.3a", 
              "name": [
                "Center for Bioinformatics, Saarland University, Saarbr\u00fccken, Germany", 
                "Max Planck Institute for Informatics, Saarbr\u00fccken, Germany", 
                "Graduate School of Computer Science, Saarland University, Saarbr\u00fccken, Germany"
              ], 
              "type": "Organization"
            }, 
            "familyName": "Ebler", 
            "givenName": "Jana", 
            "id": "sg:person.012323235077.81", 
            "sameAs": [
              "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.012323235077.81"
            ], 
            "type": "Person"
          }, 
          {
            "affiliation": {
              "alternateName": "DNAnexus, Mountain View, CA, USA", 
              "id": "http://www.grid.ac/institutes/grid.511991.4", 
              "name": [
                "DNAnexus, Mountain View, CA, USA"
              ], 
              "type": "Organization"
            }, 
            "familyName": "Fungtammasan", 
            "givenName": "Arkarachai", 
            "id": "sg:person.0602021411.13", 
            "sameAs": [
              "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0602021411.13"
            ], 
            "type": "Person"
          }, 
          {
            "affiliation": {
              "alternateName": "Google Inc., Mountain View, CA, USA", 
              "id": "http://www.grid.ac/institutes/grid.420451.6", 
              "name": [
                "Google Inc., Mountain View, CA, USA"
              ], 
              "type": "Organization"
            }, 
            "familyName": "Kolesnikov", 
            "givenName": "Alexey", 
            "type": "Person"
          }, 
          {
            "affiliation": {
              "alternateName": "National Institute of Standards and Technology, Gaithersburg, MD, USA", 
              "id": "http://www.grid.ac/institutes/grid.94225.38", 
              "name": [
                "National Institute of Standards and Technology, Gaithersburg, MD, USA"
              ], 
              "type": "Organization"
            }, 
            "familyName": "Olson", 
            "givenName": "Nathan D.", 
            "id": "sg:person.01052711105.47", 
            "sameAs": [
              "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01052711105.47"
            ], 
            "type": "Person"
          }, 
          {
            "affiliation": {
              "alternateName": "Pacific Biosciences, Menlo Park, CA, USA", 
              "id": "http://www.grid.ac/institutes/grid.423340.2", 
              "name": [
                "Pacific Biosciences, Menlo Park, CA, USA"
              ], 
              "type": "Organization"
            }, 
            "familyName": "T\u00f6pfer", 
            "givenName": "Armin", 
            "id": "sg:person.014736650413.76", 
            "sameAs": [
              "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.014736650413.76"
            ], 
            "type": "Person"
          }, 
          {
            "affiliation": {
              "alternateName": "Department of Computer Science, Johns Hopkins University, Baltimore, MD, USA", 
              "id": "http://www.grid.ac/institutes/grid.21107.35", 
              "name": [
                "Department of Computer Science, Johns Hopkins University, Baltimore, MD, USA"
              ], 
              "type": "Organization"
            }, 
            "familyName": "Alonge", 
            "givenName": "Michael", 
            "type": "Person"
          }, 
          {
            "affiliation": {
              "alternateName": "Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA", 
              "id": "http://www.grid.ac/institutes/grid.39382.33", 
              "name": [
                "Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA"
              ], 
              "type": "Organization"
            }, 
            "familyName": "Mahmoud", 
            "givenName": "Medhat", 
            "type": "Person"
          }, 
          {
            "affiliation": {
              "alternateName": "Pacific Biosciences, Menlo Park, CA, USA", 
              "id": "http://www.grid.ac/institutes/grid.423340.2", 
              "name": [
                "Pacific Biosciences, Menlo Park, CA, USA"
              ], 
              "type": "Organization"
            }, 
            "familyName": "Qian", 
            "givenName": "Yufeng", 
            "type": "Person"
          }, 
          {
            "affiliation": {
              "alternateName": "DNAnexus, Mountain View, CA, USA", 
              "id": "http://www.grid.ac/institutes/grid.511991.4", 
              "name": [
                "DNAnexus, Mountain View, CA, USA"
              ], 
              "type": "Organization"
            }, 
            "familyName": "Chin", 
            "givenName": "Chen-Shan", 
            "id": "sg:person.0703722317.20", 
            "sameAs": [
              "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0703722317.20"
            ], 
            "type": "Person"
          }, 
          {
            "affiliation": {
              "alternateName": "Genome Informatics Section, Computational and Statistical Genomics Branch, National Human Genome Research Institute, Bethesda, MD, USA", 
              "id": "http://www.grid.ac/institutes/grid.280128.1", 
              "name": [
                "Genome Informatics Section, Computational and Statistical Genomics Branch, National Human Genome Research Institute, Bethesda, MD, USA"
              ], 
              "type": "Organization"
            }, 
            "familyName": "Phillippy", 
            "givenName": "Adam M.", 
            "id": "sg:person.01337670313.24", 
            "sameAs": [
              "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01337670313.24"
            ], 
            "type": "Person"
          }, 
          {
            "affiliation": {
              "alternateName": "Department of Computer Science, Johns Hopkins University, Baltimore, MD, USA", 
              "id": "http://www.grid.ac/institutes/grid.21107.35", 
              "name": [
                "Department of Computer Science, Johns Hopkins University, Baltimore, MD, USA"
              ], 
              "type": "Organization"
            }, 
            "familyName": "Schatz", 
            "givenName": "Michael C.", 
            "id": "sg:person.0666240513.98", 
            "sameAs": [
              "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0666240513.98"
            ], 
            "type": "Person"
          }, 
          {
            "affiliation": {
              "alternateName": "Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany", 
              "id": "http://www.grid.ac/institutes/grid.419537.d", 
              "name": [
                "Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany"
              ], 
              "type": "Organization"
            }, 
            "familyName": "Myers", 
            "givenName": "Gene", 
            "id": "sg:person.0761445171.42", 
            "sameAs": [
              "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0761445171.42"
            ], 
            "type": "Person"
          }, 
          {
            "affiliation": {
              "alternateName": "Google Inc., Mountain View, CA, USA", 
              "id": "http://www.grid.ac/institutes/grid.420451.6", 
              "name": [
                "Google Inc., Mountain View, CA, USA"
              ], 
              "type": "Organization"
            }, 
            "familyName": "DePristo", 
            "givenName": "Mark A.", 
            "id": "sg:person.01174302446.46", 
            "sameAs": [
              "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01174302446.46"
            ], 
            "type": "Person"
          }, 
          {
            "affiliation": {
              "alternateName": "Agricultural Genomics Institute, Chinese Academy of Agricultural Sciences, Shenzhen, China", 
              "id": "http://www.grid.ac/institutes/grid.410727.7", 
              "name": [
                "Agricultural Genomics Institute, Chinese Academy of Agricultural Sciences, Shenzhen, China"
              ], 
              "type": "Organization"
            }, 
            "familyName": "Ruan", 
            "givenName": "Jue", 
            "id": "sg:person.0775640753.96", 
            "sameAs": [
              "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0775640753.96"
            ], 
            "type": "Person"
          }, 
          {
            "affiliation": {
              "alternateName": "Max Planck Institute for Informatics, Saarbr\u00fccken, Germany", 
              "id": "http://www.grid.ac/institutes/grid.419528.3", 
              "name": [
                "Center for Bioinformatics, Saarland University, Saarbr\u00fccken, Germany", 
                "Max Planck Institute for Informatics, Saarbr\u00fccken, Germany"
              ], 
              "type": "Organization"
            }, 
            "familyName": "Marschall", 
            "givenName": "Tobias", 
            "id": "sg:person.0657025762.22", 
            "sameAs": [
              "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0657025762.22"
            ], 
            "type": "Person"
          }, 
          {
            "affiliation": {
              "alternateName": "Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA", 
              "id": "http://www.grid.ac/institutes/grid.39382.33", 
              "name": [
                "Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA"
              ], 
              "type": "Organization"
            }, 
            "familyName": "Sedlazeck", 
            "givenName": "Fritz J.", 
            "id": "sg:person.0606351331.56", 
            "sameAs": [
              "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0606351331.56"
            ], 
            "type": "Person"
          }, 
          {
            "affiliation": {
              "alternateName": "National Institute of Standards and Technology, Gaithersburg, MD, USA", 
              "id": "http://www.grid.ac/institutes/grid.94225.38", 
              "name": [
                "National Institute of Standards and Technology, Gaithersburg, MD, USA"
              ], 
              "type": "Organization"
            }, 
            "familyName": "Zook", 
            "givenName": "Justin M.", 
            "id": "sg:person.01040401176.42", 
            "sameAs": [
              "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01040401176.42"
            ], 
            "type": "Person"
          }, 
          {
            "affiliation": {
              "alternateName": "Dana-Farber Cancer Institute, Boston, MA, USA", 
              "id": "http://www.grid.ac/institutes/grid.65499.37", 
              "name": [
                "Dana-Farber Cancer Institute, Boston, MA, USA"
              ], 
              "type": "Organization"
            }, 
            "familyName": "Li", 
            "givenName": "Heng", 
            "id": "sg:person.01043045063.88", 
            "sameAs": [
              "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01043045063.88"
            ], 
            "type": "Person"
          }, 
          {
            "affiliation": {
              "alternateName": "Genome Informatics Section, Computational and Statistical Genomics Branch, National Human Genome Research Institute, Bethesda, MD, USA", 
              "id": "http://www.grid.ac/institutes/grid.280128.1", 
              "name": [
                "Genome Informatics Section, Computational and Statistical Genomics Branch, National Human Genome Research Institute, Bethesda, MD, USA"
              ], 
              "type": "Organization"
            }, 
            "familyName": "Koren", 
            "givenName": "Sergey", 
            "id": "sg:person.01342125676.40", 
            "sameAs": [
              "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01342125676.40"
            ], 
            "type": "Person"
          }, 
          {
            "affiliation": {
              "alternateName": "Google Inc., Mountain View, CA, USA", 
              "id": "http://www.grid.ac/institutes/grid.420451.6", 
              "name": [
                "Google Inc., Mountain View, CA, USA"
              ], 
              "type": "Organization"
            }, 
            "familyName": "Carroll", 
            "givenName": "Andrew", 
            "type": "Person"
          }, 
          {
            "affiliation": {
              "alternateName": "Pacific Biosciences, Menlo Park, CA, USA", 
              "id": "http://www.grid.ac/institutes/grid.423340.2", 
              "name": [
                "Pacific Biosciences, Menlo Park, CA, USA"
              ], 
              "type": "Organization"
            }, 
            "familyName": "Rank", 
            "givenName": "David R.", 
            "id": "sg:person.0766465325.51", 
            "sameAs": [
              "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0766465325.51"
            ], 
            "type": "Person"
          }, 
          {
            "affiliation": {
              "alternateName": "Pacific Biosciences, Menlo Park, CA, USA", 
              "id": "http://www.grid.ac/institutes/grid.423340.2", 
              "name": [
                "Pacific Biosciences, Menlo Park, CA, USA"
              ], 
              "type": "Organization"
            }, 
            "familyName": "Hunkapiller", 
            "givenName": "Michael W.", 
            "id": "sg:person.01144771144.83", 
            "sameAs": [
              "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01144771144.83"
            ], 
            "type": "Person"
          }
        ], 
        "citation": [
          {
            "id": "sg:pub.10.1038/nature13907", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1014139802", 
              "https://doi.org/10.1038/nature13907"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1038/s41467-019-09025-z", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1112475979", 
              "https://doi.org/10.1038/s41467-019-09025-z"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1038/s41592-019-0669-3", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1123221691", 
              "https://doi.org/10.1038/s41592-019-0669-3"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1007/978-1-4939-8546-3_9", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1104350517", 
              "https://doi.org/10.1007/978-1-4939-8546-3_9"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1007/978-3-662-44753-6_5", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1027014678", 
              "https://doi.org/10.1007/978-3-662-44753-6_5"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1038/s41467-017-01343-4", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1092462788", 
              "https://doi.org/10.1038/s41467-017-01343-4"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1038/s41576-018-0003-4", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1101824323", 
              "https://doi.org/10.1038/s41576-018-0003-4"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1038/nmeth.2474", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1002897135", 
              "https://doi.org/10.1038/nmeth.2474"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1038/s41587-019-0074-6", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1113157788", 
              "https://doi.org/10.1038/s41587-019-0074-6"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1038/nature10242", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1007480955", 
              "https://doi.org/10.1038/nature10242"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1038/35048692", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1044298669", 
              "https://doi.org/10.1038/35048692"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1038/nature15393", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1021812064", 
              "https://doi.org/10.1038/nature15393"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1038/nbt.4235", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1107188663", 
              "https://doi.org/10.1038/nbt.4235"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1186/s12864-018-4611-3", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1101775036", 
              "https://doi.org/10.1186/s12864-018-4611-3"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1038/s41592-018-0054-7", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1105534003", 
              "https://doi.org/10.1038/s41592-018-0054-7"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1038/ng.806", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1010244476", 
              "https://doi.org/10.1038/ng.806"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1038/nbt.4060", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1100685340", 
              "https://doi.org/10.1038/nbt.4060"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1038/gim.2016.58", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1034513532", 
              "https://doi.org/10.1038/gim.2016.58"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1038/321674a0", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1041827788", 
              "https://doi.org/10.1038/321674a0"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1038/nmeth.4035", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1019059120", 
              "https://doi.org/10.1038/nmeth.4035"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1038/s41467-018-08148-z", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1113482416", 
              "https://doi.org/10.1038/s41467-018-08148-z"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1038/s41592-018-0001-7", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1103690602", 
              "https://doi.org/10.1038/s41592-018-0001-7"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1038/nbt.4277", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1107761163", 
              "https://doi.org/10.1038/nbt.4277"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1038/nature01262", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1039854529", 
              "https://doi.org/10.1038/nature01262"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1038/s41587-019-0054-x", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1112678001", 
              "https://doi.org/10.1038/s41587-019-0054-x"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1038/nature07517", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1052925719", 
              "https://doi.org/10.1038/nature07517"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1038/ncomms14061", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1074193072", 
              "https://doi.org/10.1038/ncomms14061"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1038/s41592-018-0236-3", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1110453072", 
              "https://doi.org/10.1038/s41592-018-0236-3"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1038/sdata.2016.25", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1041924932", 
              "https://doi.org/10.1038/sdata.2016.25"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1038/35057062", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1042854081", 
              "https://doi.org/10.1038/35057062"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1038/nature20098", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1049863914", 
              "https://doi.org/10.1038/nature20098"
            ], 
            "type": "CreativeWork"
          }
        ], 
        "datePublished": "2019-08-12", 
        "datePublishedReg": "2019-08-12", 
        "description": "The DNA sequencing technologies in use today produce either highly accurate short reads or less-accurate long reads. We report the optimization of circular consensus sequencing (CCS) to improve the accuracy of single-molecule real-time (SMRT) sequencing (PacBio) and generate highly accurate (99.8%) long high-fidelity (HiFi) reads with an average length of 13.5\u2009kilobases (kb). We applied our approach to sequence the well-characterized human HG002/NA24385 genome and obtained precision and recall rates of at least 99.91% for single-nucleotide variants (SNVs), 95.98% for insertions and deletions <50 bp (indels) and 95.99% for structural variants. Our CCS method matches or exceeds the ability of short-read sequencing to detect small variants and structural variants. We estimate that 2,434 discordances are correctable mistakes in the \u2018genome in a bottle\u2019 (GIAB) benchmark set. Nearly all (99.64%) variants can be phased into haplotypes, further improving variant detection. De novo genome assembly using CCS reads alone produced a contiguous and accurate genome with a contig N50 of >15\u2009megabases (Mb) and concordance of 99.997%, substantially outperforming assembly with less-accurate long reads.", 
        "genre": "article", 
        "id": "sg:pub.10.1038/s41587-019-0217-9", 
        "isAccessibleForFree": true, 
        "isFundedItemOf": [
          {
            "id": "sg:grant.7552305", 
            "type": "MonetaryGrant"
          }, 
          {
            "id": "sg:grant.3581692", 
            "type": "MonetaryGrant"
          }, 
          {
            "id": "sg:grant.5020122", 
            "type": "MonetaryGrant"
          }, 
          {
            "id": "sg:grant.8190808", 
            "type": "MonetaryGrant"
          }, 
          {
            "id": "sg:grant.2529453", 
            "type": "MonetaryGrant"
          }, 
          {
            "id": "sg:grant.7517835", 
            "type": "MonetaryGrant"
          }, 
          {
            "id": "sg:grant.8909224", 
            "type": "MonetaryGrant"
          }, 
          {
            "id": "sg:grant.6500723", 
            "type": "MonetaryGrant"
          }, 
          {
            "id": "sg:grant.7518282", 
            "type": "MonetaryGrant"
          }, 
          {
            "id": "sg:grant.4730139", 
            "type": "MonetaryGrant"
          }
        ], 
        "isPartOf": [
          {
            "id": "sg:journal.1115214", 
            "issn": [
              "1087-0156", 
              "1546-1696"
            ], 
            "name": "Nature Biotechnology", 
            "publisher": "Springer Nature", 
            "type": "Periodical"
          }, 
          {
            "issueNumber": "10", 
            "type": "PublicationIssue"
          }, 
          {
            "type": "PublicationVolume", 
            "volumeNumber": "37"
          }
        ], 
        "keywords": [
          "circular consensus sequencing", 
          "single nucleotide variants", 
          "single-molecule real-time sequencing", 
          "long reads", 
          "structural variants", 
          "de novo genome assembly", 
          "real-time sequencing", 
          "novo genome assembly", 
          "DNA sequencing technologies", 
          "contig N50", 
          "variant detection", 
          "genome assembly", 
          "human genome", 
          "sequencing technologies", 
          "CCS reads", 
          "genome", 
          "short reads", 
          "accurate genome", 
          "sequencing", 
          "consensus sequencing", 
          "reads", 
          "small variants", 
          "accurate short reads", 
          "assembly", 
          "variants", 
          "N50", 
          "megabases", 
          "kilobases", 
          "deletion", 
          "haplotypes", 
          "BP", 
          "average length", 
          "insertion", 
          "benchmark set", 
          "ability", 
          "discordance", 
          "length", 
          "concordance", 
          "detection", 
          "set", 
          "rate", 
          "approach", 
          "use today", 
          "CCS method", 
          "technology", 
          "consensus", 
          "today", 
          "bottles", 
          "method", 
          "precision", 
          "optimization", 
          "mistakes", 
          "accuracy"
        ], 
        "name": "Accurate circular consensus long-read sequencing improves variant detection and assembly of a human genome", 
        "pagination": "1155-1162", 
        "productId": [
          {
            "name": "dimensions_id", 
            "type": "PropertyValue", 
            "value": [
              "pub.1120285368"
            ]
          }, 
          {
            "name": "doi", 
            "type": "PropertyValue", 
            "value": [
              "10.1038/s41587-019-0217-9"
            ]
          }, 
          {
            "name": "pubmed_id", 
            "type": "PropertyValue", 
            "value": [
              "31406327"
            ]
          }
        ], 
        "sameAs": [
          "https://doi.org/10.1038/s41587-019-0217-9", 
          "https://app.dimensions.ai/details/publication/pub.1120285368"
        ], 
        "sdDataset": "articles", 
        "sdDatePublished": "2022-11-24T21:04", 
        "sdLicense": "https://scigraph.springernature.com/explorer/license/", 
        "sdPublisher": {
          "name": "Springer Nature - SN SciGraph project", 
          "type": "Organization"
        }, 
        "sdSource": "s3://com-springernature-scigraph/baseset/20221124/entities/gbq_results/article/article_800.jsonl", 
        "type": "ScholarlyArticle", 
        "url": "https://doi.org/10.1038/s41587-019-0217-9"
      }
    ]
     

    Download the RDF metadata as:  json-ld nt turtle xml License info

    HOW TO GET THIS DATA PROGRAMMATICALLY:

    JSON-LD is a popular format for linked data which is fully compatible with JSON.

    curl -H 'Accept: application/ld+json' 'https://scigraph.springernature.com/pub.10.1038/s41587-019-0217-9'

    N-Triples is a line-based linked data format ideal for batch operations.

    curl -H 'Accept: application/n-triples' 'https://scigraph.springernature.com/pub.10.1038/s41587-019-0217-9'

    Turtle is a human-readable linked data format.

    curl -H 'Accept: text/turtle' 'https://scigraph.springernature.com/pub.10.1038/s41587-019-0217-9'

    RDF/XML is a standard XML format for linked data.

    curl -H 'Accept: application/rdf+xml' 'https://scigraph.springernature.com/pub.10.1038/s41587-019-0217-9'


     

    This table displays all metadata directly associated to this object as RDF triples.

    509 TRIPLES      21 PREDICATES      117 URIs      78 LITERALS      15 BLANK NODES

    Subject Predicate Object
    1 sg:pub.10.1038/s41587-019-0217-9 schema:about N170376a399a244f3a5282e54dcdd88fa
    2 N5bb0c9573e5540c9a92ac9386e880b8f
    3 N60eedffcce664ba6a4a83667fc847074
    4 N66fbf55874e944f18a588251b15f53ae
    5 Nc14f450ced1241f88597f0a131ab2d28
    6 Nedb0c94d4eaf4b7890cfcbf0300142ee
    7 Nf0f126e866a642579da374410c78bccd
    8 Nf3ed98676e874a5aaddcc94140e15b46
    9 anzsrc-for:06
    10 anzsrc-for:0604
    11 schema:author N86b5fdfacf6c4b7fa26e50facdb1ade6
    12 schema:citation sg:pub.10.1007/978-1-4939-8546-3_9
    13 sg:pub.10.1007/978-3-662-44753-6_5
    14 sg:pub.10.1038/321674a0
    15 sg:pub.10.1038/35048692
    16 sg:pub.10.1038/35057062
    17 sg:pub.10.1038/gim.2016.58
    18 sg:pub.10.1038/nature01262
    19 sg:pub.10.1038/nature07517
    20 sg:pub.10.1038/nature10242
    21 sg:pub.10.1038/nature13907
    22 sg:pub.10.1038/nature15393
    23 sg:pub.10.1038/nature20098
    24 sg:pub.10.1038/nbt.4060
    25 sg:pub.10.1038/nbt.4235
    26 sg:pub.10.1038/nbt.4277
    27 sg:pub.10.1038/ncomms14061
    28 sg:pub.10.1038/ng.806
    29 sg:pub.10.1038/nmeth.2474
    30 sg:pub.10.1038/nmeth.4035
    31 sg:pub.10.1038/s41467-017-01343-4
    32 sg:pub.10.1038/s41467-018-08148-z
    33 sg:pub.10.1038/s41467-019-09025-z
    34 sg:pub.10.1038/s41576-018-0003-4
    35 sg:pub.10.1038/s41587-019-0054-x
    36 sg:pub.10.1038/s41587-019-0074-6
    37 sg:pub.10.1038/s41592-018-0001-7
    38 sg:pub.10.1038/s41592-018-0054-7
    39 sg:pub.10.1038/s41592-018-0236-3
    40 sg:pub.10.1038/s41592-019-0669-3
    41 sg:pub.10.1038/sdata.2016.25
    42 sg:pub.10.1186/s12864-018-4611-3
    43 schema:datePublished 2019-08-12
    44 schema:datePublishedReg 2019-08-12
    45 schema:description The DNA sequencing technologies in use today produce either highly accurate short reads or less-accurate long reads. We report the optimization of circular consensus sequencing (CCS) to improve the accuracy of single-molecule real-time (SMRT) sequencing (PacBio) and generate highly accurate (99.8%) long high-fidelity (HiFi) reads with an average length of 13.5 kilobases (kb). We applied our approach to sequence the well-characterized human HG002/NA24385 genome and obtained precision and recall rates of at least 99.91% for single-nucleotide variants (SNVs), 95.98% for insertions and deletions <50 bp (indels) and 95.99% for structural variants. Our CCS method matches or exceeds the ability of short-read sequencing to detect small variants and structural variants. We estimate that 2,434 discordances are correctable mistakes in the ‘genome in a bottle’ (GIAB) benchmark set. Nearly all (99.64%) variants can be phased into haplotypes, further improving variant detection. De novo genome assembly using CCS reads alone produced a contiguous and accurate genome with a contig N50 of >15 megabases (Mb) and concordance of 99.997%, substantially outperforming assembly with less-accurate long reads.
    46 schema:genre article
    47 schema:isAccessibleForFree true
    48 schema:isPartOf N55691cb628d94982ba57a6548dc140ef
    49 Na8cf8322e82f4737b0f47324e410c4b0
    50 sg:journal.1115214
    51 schema:keywords BP
    52 CCS method
    53 CCS reads
    54 DNA sequencing technologies
    55 N50
    56 ability
    57 accuracy
    58 accurate genome
    59 accurate short reads
    60 approach
    61 assembly
    62 average length
    63 benchmark set
    64 bottles
    65 circular consensus sequencing
    66 concordance
    67 consensus
    68 consensus sequencing
    69 contig N50
    70 de novo genome assembly
    71 deletion
    72 detection
    73 discordance
    74 genome
    75 genome assembly
    76 haplotypes
    77 human genome
    78 insertion
    79 kilobases
    80 length
    81 long reads
    82 megabases
    83 method
    84 mistakes
    85 novo genome assembly
    86 optimization
    87 precision
    88 rate
    89 reads
    90 real-time sequencing
    91 sequencing
    92 sequencing technologies
    93 set
    94 short reads
    95 single nucleotide variants
    96 single-molecule real-time sequencing
    97 small variants
    98 structural variants
    99 technology
    100 today
    101 use today
    102 variant detection
    103 variants
    104 schema:name Accurate circular consensus long-read sequencing improves variant detection and assembly of a human genome
    105 schema:pagination 1155-1162
    106 schema:productId N19f55855e79d410089b038465e2d3824
    107 N8142b70563dd4c929f0fa22e8fc91b30
    108 Nf5de051cca1747629c8d723cacb18705
    109 schema:sameAs https://app.dimensions.ai/details/publication/pub.1120285368
    110 https://doi.org/10.1038/s41587-019-0217-9
    111 schema:sdDatePublished 2022-11-24T21:04
    112 schema:sdLicense https://scigraph.springernature.com/explorer/license/
    113 schema:sdPublisher Nedaf3a71affe4c7d9e4132a8c312f814
    114 schema:url https://doi.org/10.1038/s41587-019-0217-9
    115 sgo:license sg:explorer/license/
    116 sgo:sdDataset articles
    117 rdf:type schema:ScholarlyArticle
    118 N0602c7ccd2ea4dfc896ffdeb4a2dcd8e schema:affiliation grid-institutes:grid.420451.6
    119 schema:familyName Kolesnikov
    120 schema:givenName Alexey
    121 rdf:type schema:Person
    122 N0a6b008d4d8846f9a5248e8ecf897a9a rdf:first sg:person.01144771144.83
    123 rdf:rest rdf:nil
    124 N15c72c45136844e3a775886d0810137b rdf:first sg:person.0602021411.13
    125 rdf:rest N6e96c5548c7f479ebbf20151fd43c9cf
    126 N170376a399a244f3a5282e54dcdd88fa schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
    127 schema:name Humans
    128 rdf:type schema:DefinedTerm
    129 N19f55855e79d410089b038465e2d3824 schema:name doi
    130 schema:value 10.1038/s41587-019-0217-9
    131 rdf:type schema:PropertyValue
    132 N2ea8ff941fa544e999fcd98ca00d424c rdf:first sg:person.01052711105.47
    133 rdf:rest N5aa6ea570ae2488dbeca9c59f67eecf9
    134 N304963f62dbe4c52b0c07e9edbd6c3e2 rdf:first sg:person.012323235077.81
    135 rdf:rest N15c72c45136844e3a775886d0810137b
    136 N33b8c1a6029e4e6fa6123d6ffc91e74f rdf:first sg:person.012731257213.44
    137 rdf:rest N8c58a54f804c49048ba9bb2b793eb873
    138 N46402f9949d24c9ea217dda95c563e49 rdf:first sg:person.01043045063.88
    139 rdf:rest Nd74f9a0170ca418fabaafae069cd2651
    140 N490d265438de4d489d414291310b233e schema:affiliation grid-institutes:grid.39382.33
    141 schema:familyName Mahmoud
    142 schema:givenName Medhat
    143 rdf:type schema:Person
    144 N49693585021749dd9eff6f41d79d8ba4 rdf:first sg:person.0703722317.20
    145 rdf:rest N51efe28954714d72897f9e05e9d47ea7
    146 N51efe28954714d72897f9e05e9d47ea7 rdf:first sg:person.01337670313.24
    147 rdf:rest Na1f051c5e3d9428eaa902722e5dd9d33
    148 N53135931f0cb46ff98ae10a61e17129e rdf:first sg:person.0655453307.39
    149 rdf:rest N304963f62dbe4c52b0c07e9edbd6c3e2
    150 N55691cb628d94982ba57a6548dc140ef schema:issueNumber 10
    151 rdf:type schema:PublicationIssue
    152 N599092b5b56a460ab08ed724174966a5 schema:affiliation grid-institutes:grid.423340.2
    153 schema:familyName Qian
    154 schema:givenName Yufeng
    155 rdf:type schema:Person
    156 N5aa6ea570ae2488dbeca9c59f67eecf9 rdf:first sg:person.014736650413.76
    157 rdf:rest N6bb57fd090114ca094fb6656a5172a0f
    158 N5bb0c9573e5540c9a92ac9386e880b8f schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
    159 schema:name Genome, Human
    160 rdf:type schema:DefinedTerm
    161 N60eedffcce664ba6a4a83667fc847074 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
    162 schema:name DNA, Circular
    163 rdf:type schema:DefinedTerm
    164 N62b276b3f289435ca8d64a28a89df350 rdf:first Nf6c8773f9c6144f4b8cc29402dc6fec3
    165 rdf:rest Nb0731883503a4986a93604a3944051be
    166 N66fbf55874e944f18a588251b15f53ae schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
    167 schema:name Sequence Analysis, DNA
    168 rdf:type schema:DefinedTerm
    169 N6bb57fd090114ca094fb6656a5172a0f rdf:first N7c0bfdcba1264ff9b10fc36e225407c4
    170 rdf:rest Nc54bdb980e014f93be8e6e1ebee860ab
    171 N6e96c5548c7f479ebbf20151fd43c9cf rdf:first N0602c7ccd2ea4dfc896ffdeb4a2dcd8e
    172 rdf:rest N2ea8ff941fa544e999fcd98ca00d424c
    173 N70a6d1d594424bf4b83bdbb2cc7da8b8 rdf:first sg:person.0775640753.96
    174 rdf:rest Nd1ddbe09639444dcb98b5e3d41d2fcdf
    175 N77c36eb408854f2f8053252adc4e3fd5 rdf:first sg:person.012465005413.81
    176 rdf:rest N33b8c1a6029e4e6fa6123d6ffc91e74f
    177 N7c0bfdcba1264ff9b10fc36e225407c4 schema:affiliation grid-institutes:grid.21107.35
    178 schema:familyName Alonge
    179 schema:givenName Michael
    180 rdf:type schema:Person
    181 N7db400fcad424792b269c7c0e67776ba rdf:first sg:person.01040401176.42
    182 rdf:rest N46402f9949d24c9ea217dda95c563e49
    183 N8142b70563dd4c929f0fa22e8fc91b30 schema:name dimensions_id
    184 schema:value pub.1120285368
    185 rdf:type schema:PropertyValue
    186 N83a5fe3b99dd4ac1bac86b6fe00cc08e rdf:first sg:person.01145166025.52
    187 rdf:rest N77c36eb408854f2f8053252adc4e3fd5
    188 N86b5fdfacf6c4b7fa26e50facdb1ade6 rdf:first sg:person.012106407613.52
    189 rdf:rest N83a5fe3b99dd4ac1bac86b6fe00cc08e
    190 N8c58a54f804c49048ba9bb2b793eb873 rdf:first Na2de3f59b8ba4fb6bdf6378cf924ba05
    191 rdf:rest N53135931f0cb46ff98ae10a61e17129e
    192 Na1f051c5e3d9428eaa902722e5dd9d33 rdf:first sg:person.0666240513.98
    193 rdf:rest Nd5dfb7c1140d44958f437aa6b3a76116
    194 Na2de3f59b8ba4fb6bdf6378cf924ba05 schema:affiliation grid-institutes:grid.423340.2
    195 schema:familyName Hall
    196 schema:givenName Richard J.
    197 rdf:type schema:Person
    198 Na77a355227524a0abe6787a2cb4d0794 rdf:first N599092b5b56a460ab08ed724174966a5
    199 rdf:rest N49693585021749dd9eff6f41d79d8ba4
    200 Na8cf8322e82f4737b0f47324e410c4b0 schema:volumeNumber 37
    201 rdf:type schema:PublicationVolume
    202 Nb0731883503a4986a93604a3944051be rdf:first sg:person.0766465325.51
    203 rdf:rest N0a6b008d4d8846f9a5248e8ecf897a9a
    204 Nc14f450ced1241f88597f0a131ab2d28 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
    205 schema:name Genetic Variation
    206 rdf:type schema:DefinedTerm
    207 Nc53a9e8900224d2c80e68998cea7b0b4 rdf:first sg:person.0606351331.56
    208 rdf:rest N7db400fcad424792b269c7c0e67776ba
    209 Nc54bdb980e014f93be8e6e1ebee860ab rdf:first N490d265438de4d489d414291310b233e
    210 rdf:rest Na77a355227524a0abe6787a2cb4d0794
    211 Nd1ddbe09639444dcb98b5e3d41d2fcdf rdf:first sg:person.0657025762.22
    212 rdf:rest Nc53a9e8900224d2c80e68998cea7b0b4
    213 Nd5dfb7c1140d44958f437aa6b3a76116 rdf:first sg:person.0761445171.42
    214 rdf:rest Ne31fbff4ad3a420a8f623cb9cfd55c29
    215 Nd74f9a0170ca418fabaafae069cd2651 rdf:first sg:person.01342125676.40
    216 rdf:rest N62b276b3f289435ca8d64a28a89df350
    217 Ne31fbff4ad3a420a8f623cb9cfd55c29 rdf:first sg:person.01174302446.46
    218 rdf:rest N70a6d1d594424bf4b83bdbb2cc7da8b8
    219 Nedaf3a71affe4c7d9e4132a8c312f814 schema:name Springer Nature - SN SciGraph project
    220 rdf:type schema:Organization
    221 Nedb0c94d4eaf4b7890cfcbf0300142ee schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
    222 schema:name Haplotypes
    223 rdf:type schema:DefinedTerm
    224 Nf0f126e866a642579da374410c78bccd schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
    225 schema:name Base Sequence
    226 rdf:type schema:DefinedTerm
    227 Nf3ed98676e874a5aaddcc94140e15b46 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
    228 schema:name High-Throughput Nucleotide Sequencing
    229 rdf:type schema:DefinedTerm
    230 Nf5de051cca1747629c8d723cacb18705 schema:name pubmed_id
    231 schema:value 31406327
    232 rdf:type schema:PropertyValue
    233 Nf6c8773f9c6144f4b8cc29402dc6fec3 schema:affiliation grid-institutes:grid.420451.6
    234 schema:familyName Carroll
    235 schema:givenName Andrew
    236 rdf:type schema:Person
    237 anzsrc-for:06 schema:inDefinedTermSet anzsrc-for:
    238 schema:name Biological Sciences
    239 rdf:type schema:DefinedTerm
    240 anzsrc-for:0604 schema:inDefinedTermSet anzsrc-for:
    241 schema:name Genetics
    242 rdf:type schema:DefinedTerm
    243 sg:grant.2529453 http://pending.schema.org/fundedItem sg:pub.10.1038/s41587-019-0217-9
    244 rdf:type schema:MonetaryGrant
    245 sg:grant.3581692 http://pending.schema.org/fundedItem sg:pub.10.1038/s41587-019-0217-9
    246 rdf:type schema:MonetaryGrant
    247 sg:grant.4730139 http://pending.schema.org/fundedItem sg:pub.10.1038/s41587-019-0217-9
    248 rdf:type schema:MonetaryGrant
    249 sg:grant.5020122 http://pending.schema.org/fundedItem sg:pub.10.1038/s41587-019-0217-9
    250 rdf:type schema:MonetaryGrant
    251 sg:grant.6500723 http://pending.schema.org/fundedItem sg:pub.10.1038/s41587-019-0217-9
    252 rdf:type schema:MonetaryGrant
    253 sg:grant.7517835 http://pending.schema.org/fundedItem sg:pub.10.1038/s41587-019-0217-9
    254 rdf:type schema:MonetaryGrant
    255 sg:grant.7518282 http://pending.schema.org/fundedItem sg:pub.10.1038/s41587-019-0217-9
    256 rdf:type schema:MonetaryGrant
    257 sg:grant.7552305 http://pending.schema.org/fundedItem sg:pub.10.1038/s41587-019-0217-9
    258 rdf:type schema:MonetaryGrant
    259 sg:grant.8190808 http://pending.schema.org/fundedItem sg:pub.10.1038/s41587-019-0217-9
    260 rdf:type schema:MonetaryGrant
    261 sg:grant.8909224 http://pending.schema.org/fundedItem sg:pub.10.1038/s41587-019-0217-9
    262 rdf:type schema:MonetaryGrant
    263 sg:journal.1115214 schema:issn 1087-0156
    264 1546-1696
    265 schema:name Nature Biotechnology
    266 schema:publisher Springer Nature
    267 rdf:type schema:Periodical
    268 sg:person.01040401176.42 schema:affiliation grid-institutes:grid.94225.38
    269 schema:familyName Zook
    270 schema:givenName Justin M.
    271 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01040401176.42
    272 rdf:type schema:Person
    273 sg:person.01043045063.88 schema:affiliation grid-institutes:grid.65499.37
    274 schema:familyName Li
    275 schema:givenName Heng
    276 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01043045063.88
    277 rdf:type schema:Person
    278 sg:person.01052711105.47 schema:affiliation grid-institutes:grid.94225.38
    279 schema:familyName Olson
    280 schema:givenName Nathan D.
    281 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01052711105.47
    282 rdf:type schema:Person
    283 sg:person.01144771144.83 schema:affiliation grid-institutes:grid.423340.2
    284 schema:familyName Hunkapiller
    285 schema:givenName Michael W.
    286 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01144771144.83
    287 rdf:type schema:Person
    288 sg:person.01145166025.52 schema:affiliation grid-institutes:grid.423340.2
    289 schema:familyName Peluso
    290 schema:givenName Paul
    291 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01145166025.52
    292 rdf:type schema:Person
    293 sg:person.01174302446.46 schema:affiliation grid-institutes:grid.420451.6
    294 schema:familyName DePristo
    295 schema:givenName Mark A.
    296 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01174302446.46
    297 rdf:type schema:Person
    298 sg:person.012106407613.52 schema:affiliation grid-institutes:grid.423340.2
    299 schema:familyName Wenger
    300 schema:givenName Aaron M.
    301 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.012106407613.52
    302 rdf:type schema:Person
    303 sg:person.012323235077.81 schema:affiliation grid-institutes:grid.11749.3a
    304 schema:familyName Ebler
    305 schema:givenName Jana
    306 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.012323235077.81
    307 rdf:type schema:Person
    308 sg:person.012465005413.81 schema:affiliation grid-institutes:grid.423340.2
    309 schema:familyName Rowell
    310 schema:givenName William J.
    311 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.012465005413.81
    312 rdf:type schema:Person
    313 sg:person.012731257213.44 schema:affiliation grid-institutes:grid.420451.6
    314 schema:familyName Chang
    315 schema:givenName Pi-Chuan
    316 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.012731257213.44
    317 rdf:type schema:Person
    318 sg:person.01337670313.24 schema:affiliation grid-institutes:grid.280128.1
    319 schema:familyName Phillippy
    320 schema:givenName Adam M.
    321 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01337670313.24
    322 rdf:type schema:Person
    323 sg:person.01342125676.40 schema:affiliation grid-institutes:grid.280128.1
    324 schema:familyName Koren
    325 schema:givenName Sergey
    326 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01342125676.40
    327 rdf:type schema:Person
    328 sg:person.014736650413.76 schema:affiliation grid-institutes:grid.423340.2
    329 schema:familyName Töpfer
    330 schema:givenName Armin
    331 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.014736650413.76
    332 rdf:type schema:Person
    333 sg:person.0602021411.13 schema:affiliation grid-institutes:grid.511991.4
    334 schema:familyName Fungtammasan
    335 schema:givenName Arkarachai
    336 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0602021411.13
    337 rdf:type schema:Person
    338 sg:person.0606351331.56 schema:affiliation grid-institutes:grid.39382.33
    339 schema:familyName Sedlazeck
    340 schema:givenName Fritz J.
    341 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0606351331.56
    342 rdf:type schema:Person
    343 sg:person.0655453307.39 schema:affiliation grid-institutes:grid.423340.2
    344 schema:familyName Concepcion
    345 schema:givenName Gregory T.
    346 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0655453307.39
    347 rdf:type schema:Person
    348 sg:person.0657025762.22 schema:affiliation grid-institutes:grid.419528.3
    349 schema:familyName Marschall
    350 schema:givenName Tobias
    351 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0657025762.22
    352 rdf:type schema:Person
    353 sg:person.0666240513.98 schema:affiliation grid-institutes:grid.21107.35
    354 schema:familyName Schatz
    355 schema:givenName Michael C.
    356 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0666240513.98
    357 rdf:type schema:Person
    358 sg:person.0703722317.20 schema:affiliation grid-institutes:grid.511991.4
    359 schema:familyName Chin
    360 schema:givenName Chen-Shan
    361 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0703722317.20
    362 rdf:type schema:Person
    363 sg:person.0761445171.42 schema:affiliation grid-institutes:grid.419537.d
    364 schema:familyName Myers
    365 schema:givenName Gene
    366 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0761445171.42
    367 rdf:type schema:Person
    368 sg:person.0766465325.51 schema:affiliation grid-institutes:grid.423340.2
    369 schema:familyName Rank
    370 schema:givenName David R.
    371 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0766465325.51
    372 rdf:type schema:Person
    373 sg:person.0775640753.96 schema:affiliation grid-institutes:grid.410727.7
    374 schema:familyName Ruan
    375 schema:givenName Jue
    376 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0775640753.96
    377 rdf:type schema:Person
    378 sg:pub.10.1007/978-1-4939-8546-3_9 schema:sameAs https://app.dimensions.ai/details/publication/pub.1104350517
    379 https://doi.org/10.1007/978-1-4939-8546-3_9
    380 rdf:type schema:CreativeWork
    381 sg:pub.10.1007/978-3-662-44753-6_5 schema:sameAs https://app.dimensions.ai/details/publication/pub.1027014678
    382 https://doi.org/10.1007/978-3-662-44753-6_5
    383 rdf:type schema:CreativeWork
    384 sg:pub.10.1038/321674a0 schema:sameAs https://app.dimensions.ai/details/publication/pub.1041827788
    385 https://doi.org/10.1038/321674a0
    386 rdf:type schema:CreativeWork
    387 sg:pub.10.1038/35048692 schema:sameAs https://app.dimensions.ai/details/publication/pub.1044298669
    388 https://doi.org/10.1038/35048692
    389 rdf:type schema:CreativeWork
    390 sg:pub.10.1038/35057062 schema:sameAs https://app.dimensions.ai/details/publication/pub.1042854081
    391 https://doi.org/10.1038/35057062
    392 rdf:type schema:CreativeWork
    393 sg:pub.10.1038/gim.2016.58 schema:sameAs https://app.dimensions.ai/details/publication/pub.1034513532
    394 https://doi.org/10.1038/gim.2016.58
    395 rdf:type schema:CreativeWork
    396 sg:pub.10.1038/nature01262 schema:sameAs https://app.dimensions.ai/details/publication/pub.1039854529
    397 https://doi.org/10.1038/nature01262
    398 rdf:type schema:CreativeWork
    399 sg:pub.10.1038/nature07517 schema:sameAs https://app.dimensions.ai/details/publication/pub.1052925719
    400 https://doi.org/10.1038/nature07517
    401 rdf:type schema:CreativeWork
    402 sg:pub.10.1038/nature10242 schema:sameAs https://app.dimensions.ai/details/publication/pub.1007480955
    403 https://doi.org/10.1038/nature10242
    404 rdf:type schema:CreativeWork
    405 sg:pub.10.1038/nature13907 schema:sameAs https://app.dimensions.ai/details/publication/pub.1014139802
    406 https://doi.org/10.1038/nature13907
    407 rdf:type schema:CreativeWork
    408 sg:pub.10.1038/nature15393 schema:sameAs https://app.dimensions.ai/details/publication/pub.1021812064
    409 https://doi.org/10.1038/nature15393
    410 rdf:type schema:CreativeWork
    411 sg:pub.10.1038/nature20098 schema:sameAs https://app.dimensions.ai/details/publication/pub.1049863914
    412 https://doi.org/10.1038/nature20098
    413 rdf:type schema:CreativeWork
    414 sg:pub.10.1038/nbt.4060 schema:sameAs https://app.dimensions.ai/details/publication/pub.1100685340
    415 https://doi.org/10.1038/nbt.4060
    416 rdf:type schema:CreativeWork
    417 sg:pub.10.1038/nbt.4235 schema:sameAs https://app.dimensions.ai/details/publication/pub.1107188663
    418 https://doi.org/10.1038/nbt.4235
    419 rdf:type schema:CreativeWork
    420 sg:pub.10.1038/nbt.4277 schema:sameAs https://app.dimensions.ai/details/publication/pub.1107761163
    421 https://doi.org/10.1038/nbt.4277
    422 rdf:type schema:CreativeWork
    423 sg:pub.10.1038/ncomms14061 schema:sameAs https://app.dimensions.ai/details/publication/pub.1074193072
    424 https://doi.org/10.1038/ncomms14061
    425 rdf:type schema:CreativeWork
    426 sg:pub.10.1038/ng.806 schema:sameAs https://app.dimensions.ai/details/publication/pub.1010244476
    427 https://doi.org/10.1038/ng.806
    428 rdf:type schema:CreativeWork
    429 sg:pub.10.1038/nmeth.2474 schema:sameAs https://app.dimensions.ai/details/publication/pub.1002897135
    430 https://doi.org/10.1038/nmeth.2474
    431 rdf:type schema:CreativeWork
    432 sg:pub.10.1038/nmeth.4035 schema:sameAs https://app.dimensions.ai/details/publication/pub.1019059120
    433 https://doi.org/10.1038/nmeth.4035
    434 rdf:type schema:CreativeWork
    435 sg:pub.10.1038/s41467-017-01343-4 schema:sameAs https://app.dimensions.ai/details/publication/pub.1092462788
    436 https://doi.org/10.1038/s41467-017-01343-4
    437 rdf:type schema:CreativeWork
    438 sg:pub.10.1038/s41467-018-08148-z schema:sameAs https://app.dimensions.ai/details/publication/pub.1113482416
    439 https://doi.org/10.1038/s41467-018-08148-z
    440 rdf:type schema:CreativeWork
    441 sg:pub.10.1038/s41467-019-09025-z schema:sameAs https://app.dimensions.ai/details/publication/pub.1112475979
    442 https://doi.org/10.1038/s41467-019-09025-z
    443 rdf:type schema:CreativeWork
    444 sg:pub.10.1038/s41576-018-0003-4 schema:sameAs https://app.dimensions.ai/details/publication/pub.1101824323
    445 https://doi.org/10.1038/s41576-018-0003-4
    446 rdf:type schema:CreativeWork
    447 sg:pub.10.1038/s41587-019-0054-x schema:sameAs https://app.dimensions.ai/details/publication/pub.1112678001
    448 https://doi.org/10.1038/s41587-019-0054-x
    449 rdf:type schema:CreativeWork
    450 sg:pub.10.1038/s41587-019-0074-6 schema:sameAs https://app.dimensions.ai/details/publication/pub.1113157788
    451 https://doi.org/10.1038/s41587-019-0074-6
    452 rdf:type schema:CreativeWork
    453 sg:pub.10.1038/s41592-018-0001-7 schema:sameAs https://app.dimensions.ai/details/publication/pub.1103690602
    454 https://doi.org/10.1038/s41592-018-0001-7
    455 rdf:type schema:CreativeWork
    456 sg:pub.10.1038/s41592-018-0054-7 schema:sameAs https://app.dimensions.ai/details/publication/pub.1105534003
    457 https://doi.org/10.1038/s41592-018-0054-7
    458 rdf:type schema:CreativeWork
    459 sg:pub.10.1038/s41592-018-0236-3 schema:sameAs https://app.dimensions.ai/details/publication/pub.1110453072
    460 https://doi.org/10.1038/s41592-018-0236-3
    461 rdf:type schema:CreativeWork
    462 sg:pub.10.1038/s41592-019-0669-3 schema:sameAs https://app.dimensions.ai/details/publication/pub.1123221691
    463 https://doi.org/10.1038/s41592-019-0669-3
    464 rdf:type schema:CreativeWork
    465 sg:pub.10.1038/sdata.2016.25 schema:sameAs https://app.dimensions.ai/details/publication/pub.1041924932
    466 https://doi.org/10.1038/sdata.2016.25
    467 rdf:type schema:CreativeWork
    468 sg:pub.10.1186/s12864-018-4611-3 schema:sameAs https://app.dimensions.ai/details/publication/pub.1101775036
    469 https://doi.org/10.1186/s12864-018-4611-3
    470 rdf:type schema:CreativeWork
    471 grid-institutes:grid.11749.3a schema:alternateName Graduate School of Computer Science, Saarland University, Saarbrücken, Germany
    472 schema:name Center for Bioinformatics, Saarland University, Saarbrücken, Germany
    473 Graduate School of Computer Science, Saarland University, Saarbrücken, Germany
    474 Max Planck Institute for Informatics, Saarbrücken, Germany
    475 rdf:type schema:Organization
    476 grid-institutes:grid.21107.35 schema:alternateName Department of Computer Science, Johns Hopkins University, Baltimore, MD, USA
    477 schema:name Department of Computer Science, Johns Hopkins University, Baltimore, MD, USA
    478 rdf:type schema:Organization
    479 grid-institutes:grid.280128.1 schema:alternateName Genome Informatics Section, Computational and Statistical Genomics Branch, National Human Genome Research Institute, Bethesda, MD, USA
    480 schema:name Genome Informatics Section, Computational and Statistical Genomics Branch, National Human Genome Research Institute, Bethesda, MD, USA
    481 rdf:type schema:Organization
    482 grid-institutes:grid.39382.33 schema:alternateName Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
    483 schema:name Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
    484 rdf:type schema:Organization
    485 grid-institutes:grid.410727.7 schema:alternateName Agricultural Genomics Institute, Chinese Academy of Agricultural Sciences, Shenzhen, China
    486 schema:name Agricultural Genomics Institute, Chinese Academy of Agricultural Sciences, Shenzhen, China
    487 rdf:type schema:Organization
    488 grid-institutes:grid.419528.3 schema:alternateName Max Planck Institute for Informatics, Saarbrücken, Germany
    489 schema:name Center for Bioinformatics, Saarland University, Saarbrücken, Germany
    490 Max Planck Institute for Informatics, Saarbrücken, Germany
    491 rdf:type schema:Organization
    492 grid-institutes:grid.419537.d schema:alternateName Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
    493 schema:name Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
    494 rdf:type schema:Organization
    495 grid-institutes:grid.420451.6 schema:alternateName Google Inc., Mountain View, CA, USA
    496 schema:name Google Inc., Mountain View, CA, USA
    497 rdf:type schema:Organization
    498 grid-institutes:grid.423340.2 schema:alternateName Pacific Biosciences, Menlo Park, CA, USA
    499 schema:name Pacific Biosciences, Menlo Park, CA, USA
    500 rdf:type schema:Organization
    501 grid-institutes:grid.511991.4 schema:alternateName DNAnexus, Mountain View, CA, USA
    502 schema:name DNAnexus, Mountain View, CA, USA
    503 rdf:type schema:Organization
    504 grid-institutes:grid.65499.37 schema:alternateName Dana-Farber Cancer Institute, Boston, MA, USA
    505 schema:name Dana-Farber Cancer Institute, Boston, MA, USA
    506 rdf:type schema:Organization
    507 grid-institutes:grid.94225.38 schema:alternateName National Institute of Standards and Technology, Gaithersburg, MD, USA
    508 schema:name National Institute of Standards and Technology, Gaithersburg, MD, USA
    509 rdf:type schema:Organization
     




    Preview window. Press ESC to close (or click here)


    ...