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Volumn 36, Issue 4, 2018, Pages 338-345

Nanopore sequencing and assembly of a human genome with ultra-long reads

(26)  Jain, Miten a   Koren, Sergey b   Miga, Karen H a   Quick, Josh c   Rand, Arthur C a   Sasani, Thomas A d,e   Tyson, John R f   Beggs, Andrew D c   Dilthey, Alexander T b   Fiddes, Ian T a   Malla, Sunir g   Marriott, Hannah g   Nieto, Tom c   O'Grady, Justin h   Olsen, Hugh E a   Pedersen, Brent S d,e   Rhie, Arang b   Richardson, Hollian h   Quinlan, Aaron R d,e   Snutch, Terrance P f   more..


Author keywords

[No Author keywords available]

Indexed keywords

CELL CULTURE; NANOPORES;

EID: 85044543338     PISSN: 10870156     EISSN: 15461696     Source Type: Journal    
DOI: 10.1038/nbt.4060     Document Type: Article
Times cited : (1279)

References (70)
  • 1
    • 42249087308 scopus 로고    scopus 로고
    • The complete genome of an individual by massively parallel DNA sequencing
    • Wheeler, D.A., et al. The complete genome of an individual by massively parallel DNA sequencing. Nature 452, 872-876 (2008).
    • (2008) Nature , vol.452 , pp. 872-876
    • Wheeler, D.A.1
  • 2
    • 55549089660 scopus 로고    scopus 로고
    • Accurate whole human genome sequencing using reversible terminator chemistry
    • Bentley, D.R., et al. Accurate whole human genome sequencing using reversible terminator chemistry. Nature 456, 53-59 (2008).
    • (2008) Nature , vol.456 , pp. 53-59
    • Bentley, D.R.1
  • 3
    • 70249089090 scopus 로고    scopus 로고
    • Single-molecule sequencing of an individual human genome
    • Pushkarev, D., Neff, N.F., Quake, S.R. Single-molecule sequencing of an individual human genome. Nat. Biotechnol. 27, 847-850 (2009).
    • (2009) Nat. Biotechnol. , vol.27 , pp. 847-850
    • Pushkarev, D.1    Neff, N.F.2    Quake, S.R.3
  • 4
    • 79960597679 scopus 로고    scopus 로고
    • An integrated semiconductor device enabling non-optical genome sequencing
    • Rothberg, J.M., et al. An integrated semiconductor device enabling non-optical genome sequencing. Nature 475, 348-352 (2011).
    • (2011) Nature , vol.475 , pp. 348-352
    • Rothberg, J.M.1
  • 5
    • 84938423867 scopus 로고    scopus 로고
    • Assembly and diploid architecture of an individual human genome via single-molecule technologies
    • Pendleton, M., et al. Assembly and diploid architecture of an individual human genome via single-molecule technologies. Nat. Methods 12, 780-786 (2015).
    • (2015) Nat. Methods , vol.12 , pp. 780-786
    • Pendleton, M.1
  • 6
    • 57049118443 scopus 로고    scopus 로고
    • Analysis of the largest tandemly repeated DNA families in the human genome
    • Warburton, P.E., et al. Analysis of the largest tandemly repeated DNA families in the human genome. BMC Genomics 9, 533 (2008).
    • (2008) BMC Genomics , vol.9 , pp. 533
    • Warburton, P.E.1
  • 7
    • 0024379003 scopus 로고
    • Long-range organization of tandem arrays of alpha satellite DNA at the centromeres of human chromosomes: High-frequency arraylength polymorphism and meiotic stability
    • Wevrick, R., Willard, H.F. Long-range organization of tandem arrays of alpha satellite DNA at the centromeres of human chromosomes: High-frequency arraylength polymorphism and meiotic stability. Proc. Natl. Acad. Sci. USA 86, 9394-9398 (1989).
    • (1989) Proc. Natl. Acad. Sci. USA , vol.86 , pp. 9394-9398
    • Wevrick, R.1    Willard, H.F.2
  • 8
    • 1942499458 scopus 로고    scopus 로고
    • An assessment of the sequence gaps: Unfinished business in a finished human genome
    • Eichler, E.E., Clark, R.A., She, X. An assessment of the sequence gaps: Unfinished business in a finished human genome. Nat. Rev. Genet. 5, 345-354 (2004).
    • (2004) Nat. Rev. Genet. , vol.5 , pp. 345-354
    • Eichler, E.E.1    Clark, R.A.2    She, X.3
  • 9
    • 84963548310 scopus 로고    scopus 로고
    • Long-read sequence assembly of the gorilla genome
    • Gordon, D., et al. Long-read sequence assembly of the gorilla genome. Science 352, aae0344 (2016).
    • (2016) Science , vol.352 , pp. aae0344
    • Gordon, D.1
  • 10
    • 84944441319 scopus 로고    scopus 로고
    • Genetic variation and the de novo assembly of human genomes
    • Chaisson, M.J.P., Wilson, R.K., Eichler, E.E. Genetic variation and the de novo assembly of human genomes. Nat. Rev. Genet. 16, 627-640 (2015).
    • (2015) Nat. Rev. Genet. , vol.16 , pp. 627-640
    • Chaisson, M.J.P.1    Wilson, R.K.2    Eichler, E.E.3
  • 11
    • 84998996876 scopus 로고    scopus 로고
    • The Oxford Nanopore MinION: Delivery of nanopore sequencing to the genomics community
    • Jain, M., Olsen, H.E., Paten, B., Akeson, M. The Oxford Nanopore MinION: Delivery of nanopore sequencing to the genomics community. Genome Biol. 17, 239 (2016).
    • (2016) Genome Biol. , vol.17 , pp. 239
    • Jain, M.1    Olsen, H.E.2    Paten, B.3    Akeson, M.4
  • 12
    • 84958068536 scopus 로고    scopus 로고
    • Real-time, portable genome sequencing for Ebola surveillance
    • Quick, J., et al. Real-time, portable genome sequencing for Ebola surveillance. Nature 530, 228-232 (2016).
    • (2016) Nature , vol.530 , pp. 228-232
    • Quick, J.1
  • 13
    • 84934284959 scopus 로고    scopus 로고
    • Rapid draft sequencing and real-time nanopore sequencing in a hospital outbreak of Salmonella
    • Quick, J., et al. Rapid draft sequencing and real-time nanopore sequencing in a hospital outbreak of Salmonella. Genome Biol. 16, 114 (2015).
    • (2015) Genome Biol. , vol.16 , pp. 114
    • Quick, J.1
  • 14
    • 84938421951 scopus 로고    scopus 로고
    • A complete bacterial genome assembled de novo using only nanopore sequencing data
    • Loman, N.J., Quick, J., Simpson, J.T. A complete bacterial genome assembled de novo using only nanopore sequencing data. Nat. Methods 12, 733-735 (2015).
    • (2015) Nat. Methods , vol.12 , pp. 733-735
    • Loman, N.J.1    Quick, J.2    Simpson, J.T.3
  • 15
    • 85021859981 scopus 로고    scopus 로고
    • De novo assembly and population genomic survey of natural yeast isolates with the Oxford Nanopore MinION sequencer
    • Istace, B., et al. de novo assembly and population genomic survey of natural yeast isolates with the Oxford Nanopore MinION sequencer. Gigascience 6, 1-13 (2017).
    • (2017) Gigascience , vol.6 , pp. 1-13
    • Istace, B.1
  • 20
    • 84976413217 scopus 로고    scopus 로고
    • Extensive sequencing of seven human genomes to characterize benchmark reference materials
    • Zook, J.M., et al. Extensive sequencing of seven human genomes to characterize benchmark reference materials. Sci. Data 3, 160025 (2016).
    • (2016) Sci. Data , vol.3 , pp. 160025
    • Zook, J.M.1
  • 21
    • 84926472171 scopus 로고    scopus 로고
    • Improved data analysis for the MinION nanopore sequencer
    • Jain, M., et al. Improved data analysis for the MinION nanopore sequencer. Nat. Methods 12, 351-356 (2015).
    • (2015) Nat. Methods , vol.12 , pp. 351-356
    • Jain, M.1
  • 23
    • 85009151993 scopus 로고    scopus 로고
    • A reference data set of 5.4 million phased human variants validated by genetic inheritance from sequencing a three-generation 17-member pedigree
    • Eberle, M.A., et al. A reference data set of 5.4 million phased human variants validated by genetic inheritance from sequencing a three-generation 17-member pedigree. Genome Res. 27, 157-164 (2017).
    • (2017) Genome Res. , vol.27 , pp. 157-164
    • Eberle, M.A.1
  • 24
    • 85019066712 scopus 로고    scopus 로고
    • Canu: Scalable and accurate long-read assembly via adaptive k-mer weighting and repeat separation
    • Koren, S., et al. Canu: Scalable and accurate long-read assembly via adaptive k-mer weighting and repeat separation. Genome Res. 27, 722-736 (2017).
    • (2017) Genome Res. , vol.27 , pp. 722-736
    • Koren, S.1
  • 25
    • 85019127944 scopus 로고    scopus 로고
    • Evaluation of GRCh38 and de novo haploid genome assemblies demonstrates the enduring quality of the reference assembly
    • Schneider, V.A., et al. Evaluation of GRCh38 and de novo haploid genome assemblies demonstrates the enduring quality of the reference assembly. Genome Res. 27, 849-864 (2017).
    • (2017) Genome Res. , vol.27 , pp. 849-864
    • Schneider, V.A.1
  • 26
    • 84914689868 scopus 로고    scopus 로고
    • Pilon: An integrated tool for comprehensive microbial variant detection and genome assembly improvement
    • Walker, B.J., et al. Pilon: An integrated tool for comprehensive microbial variant detection and genome assembly improvement. PLoS One 9, e112963 (2014).
    • (2014) PLoS One , vol.9 , pp. e112963
    • Walker, B.J.1
  • 27
    • 85014528210 scopus 로고    scopus 로고
    • Single-molecule sequencing and chromatin conformation capture enable de novo reference assembly of the domestic goat genome
    • Bickhart, D.M., et al. Single-molecule sequencing and chromatin conformation capture enable de novo reference assembly of the domestic goat genome. Nat. Genet. 49, 643-650 (2017).
    • (2017) Nat. Genet. , vol.49 , pp. 643-650
    • Bickhart, D.M.1
  • 28
    • 84959179341 scopus 로고    scopus 로고
    • SpeedSeq: Ultra-fast personal genome analysis and interpretation
    • Chiang, C., et al. SpeedSeq: Ultra-fast personal genome analysis and interpretation. Nat. Methods 12, 966-968 (2015).
    • (2015) Nat. Methods , vol.12 , pp. 966-968
    • Chiang, C.1
  • 29
    • 84912096454 scopus 로고    scopus 로고
    • LUMPY: A probabilistic framework for structural variant discovery
    • Layer, R.M., Chiang, C., Quinlan, A.R., Hall, I.M. LUMPY: A probabilistic framework for structural variant discovery. Genome Biol. 15, R84 (2014).
    • (2014) Genome Biol. , vol.15 , pp. R84
    • Layer, R.M.1    Chiang, C.2    Quinlan, A.R.3    Hall, I.M.4
  • 30
    • 84897387657 scopus 로고    scopus 로고
    • Integrating human sequence data sets provides a resource of benchmark SNP and indel genotype calls
    • Zook, J.M., et al. Integrating human sequence data sets provides a resource of benchmark SNP and indel genotype calls. Nat. Biotechnol. 32, 246-251 (2014).
    • (2014) Nat. Biotechnol. , vol.32 , pp. 246-251
    • Zook, J.M.1
  • 31
    • 78651271733 scopus 로고    scopus 로고
    • Integrative genomics viewer
    • Robinson, J.T., et al. Integrative genomics viewer. Nat. Biotechnol. 29, 24-26 (2011).
    • (2011) Nat. Biotechnol. , vol.29 , pp. 24-26
    • Robinson, J.T.1
  • 32
    • 84943171338 scopus 로고    scopus 로고
    • A global reference for human genetic variation
    • Auton, A., et al. A global reference for human genetic variation. Nature 526, 68-74 (2015).
    • (2015) Nature , vol.526 , pp. 68-74
    • Auton, A.1
  • 33
    • 84914170339 scopus 로고    scopus 로고
    • Nanopores discriminate among five C5-cytosine variants in DNA
    • Wescoe, Z.L., Schreiber, J., Akeson, M. Nanopores discriminate among five C5-cytosine variants in DNA. J. Am. Chem. Soc. 136, 16582-16587 (2014).
    • (2014) J. Am. Chem. Soc. , vol.136 , pp. 16582-16587
    • Wescoe, Z.L.1    Schreiber, J.2    Akeson, M.3
  • 34
    • 84888118119 scopus 로고    scopus 로고
    • Detection and mapping of 5-methylcytosine and 5-hydroxymethylcytosine with nanopore MspA
    • Laszlo, A.H., et al. Detection and mapping of 5-methylcytosine and 5-hydroxymethylcytosine with nanopore MspA. Proc. Natl. Acad. Sci. USA 110, 18904-18909 (2013).
    • (2013) Proc. Natl. Acad. Sci. USA , vol.110 , pp. 18904-18909
    • Laszlo, A.H.1
  • 35
    • 85013157844 scopus 로고    scopus 로고
    • Mapping DNA methylation with high-throughput nanopore sequencing
    • Rand, A.C., et al. Mapping DNA methylation with high-throughput nanopore sequencing. Nat. Methods 14, 411-413 (2017).
    • (2017) Nat. Methods , vol.14 , pp. 411-413
    • Rand, A.C.1
  • 36
    • 85013175291 scopus 로고    scopus 로고
    • Detecting DNA cytosine methylation using nanopore sequencing
    • Simpson, J.T., et al. Detecting DNA cytosine methylation using nanopore sequencing. Nat. Methods 14, 407-410 (2017).
    • (2017) Nat. Methods , vol.14 , pp. 407-410
    • Simpson, J.T.1
  • 37
    • 84964528782 scopus 로고    scopus 로고
    • Fast and sensitive mapping of nanopore sequencing reads with GraphMap
    • Sović, I., et al. Fast and sensitive mapping of nanopore sequencing reads with GraphMap. Nat. Commun. 7, 11307 (2016).
    • (2016) Nat. Commun. , vol.7 , pp. 11307
    • Sović, I.1
  • 40
    • 84994101837 scopus 로고    scopus 로고
    • High-accuracy HLA type inference from whole-genome sequencing data using population reference graphs
    • Dilthey, A.T., et al. High-accuracy HLA type inference from whole-genome sequencing data using population reference graphs. PLOS Comput. Biol. 12, e1005151 (2016).
    • (2016) PLOS Comput. Biol. , vol.12 , pp. e1005151
    • Dlthey, A.T.1
  • 41
    • 84977101027 scopus 로고    scopus 로고
    • Long-read sequencing and de novo assembly of a Chinese genome
    • Shi, L., et al. Long-read sequencing and de novo assembly of a Chinese genome. Nat. Commun. 7, 12065 (2016).
    • (2016) Nat. Commun. , vol.7 , pp. 12065
    • Shi, L.1
  • 42
    • 84991738269 scopus 로고    scopus 로고
    • De novo assembly and phasing of a Korean human genome
    • Seo, J.-S., et al. De novo assembly and phasing of a Korean human genome. Nature 538, 243-247 (2016).
    • (2016) Nature , vol.538 , pp. 243-247
    • Seo, J.-S.1
  • 43
    • 85019081248 scopus 로고    scopus 로고
    • Sequences of 95 human MHC haplotypes reveal extreme coding variation in genes other than highly polymorphic HLA class I and II
    • Norman, P.J., et al. Sequences of 95 human MHC haplotypes reveal extreme coding variation in genes other than highly polymorphic HLA class I and II. Genome Res. 27, 813-823 (2017).
    • (2017) Genome Res. , vol.27 , pp. 813-823
    • Norman, P.J.1
  • 44
    • 37549017677 scopus 로고    scopus 로고
    • Closing gaps in the human genome with fosmid resources generated from multiple individuals
    • Bovee, D., et al. Closing gaps in the human genome with fosmid resources generated from multiple individuals. Nat. Genet. 40, 96-101 (2008).
    • (2008) Nat. Genet. , vol.40 , pp. 96-101
    • Bovee, D.1
  • 45
    • 33644756521 scopus 로고    scopus 로고
    • Identification of a new cancer/testis gene family, CT47, among expressed multicopy genes on the human X chromosome
    • Chen, Y.-T., et al. Identification of a new cancer/testis gene family, CT47, among expressed multicopy genes on the human X chromosome. Genes Chromosom. Cancer 45, 392-400 (2006).
    • (2006) Genes Chromosom. Cancer , vol.45 , pp. 392-400
    • Chen, Y.-T.1
  • 46
    • 84926472171 scopus 로고    scopus 로고
    • Improved data analysis for the MinION nanopore sequencer
    • Jain, M., et al. Improved data analysis for the MinION nanopore sequencer. Nat. Methods 12, 351-356 (2015).
    • (2015) Nat. Methods , vol.12 , pp. 351-356
    • Jain, M.1
  • 47
    • 0013462065 scopus 로고
    • A highly conserved repetitive DNA sequence, (TTAGGG)n, present at the telomeres of human chromosomes
    • Moyzis, R.K., et al. A highly conserved repetitive DNA sequence, (TTAGGG)n, present at the telomeres of human chromosomes. Proc. Natl. Acad. Sci. USA 85, 6622-6626 (1988).
    • (1988) Proc. Natl. Acad. Sci. USA , vol.85 , pp. 6622-6626
    • Moyzis, R.K.1
  • 48
    • 79751503987 scopus 로고    scopus 로고
    • Measurement of telomere length by the Southern blot analysis of terminal restriction fragment lengths
    • Kimura, M., et al. Measurement of telomere length by the Southern blot analysis of terminal restriction fragment lengths. Nat. Protoc. 5, 1596-1607 (2010).
    • (2010) Nat. Protoc. , vol.5 , pp. 1596-1607
    • Kimura, M.1
  • 49
    • 85026856426 scopus 로고    scopus 로고
    • Sequencing and de novo assembly of 150 genomes from Denmark as a population reference
    • Maretty, L., et al. Sequencing and de novo assembly of 150 genomes from Denmark as a population reference. Nature 548, 87-91 (2017).
    • (2017) Nature , vol.548 , pp. 87-91
    • Maretty, L.1
  • 53
    • 84891677372 scopus 로고    scopus 로고
    • Optimal assembly for high throughput shotgun sequencing
    • Bresler, G., Bresler, M., Tse, D. Optimal assembly for high throughput shotgun sequencing. BMC Bioinformatics 14 (Suppl. 5: S18) (2013).
    • (2013) BMC Bioinformatics , vol.14
    • Bresler, G.1    Bresler, M.2    Tse, D.3
  • 54
    • 0027113212 scopus 로고
    • Approximate string-matching with q-grams and maximal matches
    • Ukkonen, E. Approximate string-matching with q-grams and maximal matches. Theor. Comput. Sci. 92, 191-211 (1992).
    • (1992) Theor. Comput. Sci. , vol.92 , pp. 191-211
    • Ukkonen, E.1
  • 55
    • 84930851165 scopus 로고    scopus 로고
    • Assembling large genomes with single-molecule sequencing and locality-sensitive hashing
    • Berlin, K., et al. Assembling large genomes with single-molecule sequencing and locality-sensitive hashing. Nat. Biotechnol. 33, 623-630 (2015).
    • (2015) Nat. Biotechnol. , vol.33 , pp. 623-630
    • Berlin, K.1
  • 58
    • 84990891493 scopus 로고    scopus 로고
    • Assemblytics: A web analytics tool for the detection of variants from an assembly
    • Nattestad, M., Schatz, M.C. Assemblytics: A web analytics tool for the detection of variants from an assembly. Bioinformatics 32, 3021-3023 (2016).
    • (2016) Bioinformatics , vol.32 , pp. 3021-3023
    • Nattestad, M.1    Schatz, M.C.2
  • 60
    • 84992371738 scopus 로고    scopus 로고
    • Minimap and miniasm: Fast mapping and de novo assembly for noisy long sequences
    • Li, H. Minimap and miniasm: Fast mapping and de novo assembly for noisy long sequences. Bioinformatics 32, 2103-2110 (2016).
    • (2016) Bioinformatics , vol.32 , pp. 2103-2110
    • Li, H.1
  • 61
    • 37849032744 scopus 로고    scopus 로고
    • Comparative genomics search for losses of long-established genes on the human lineage
    • Zhu, J., et al. Comparative genomics search for losses of long-established genes on the human lineage. PLOS Comput. Biol. 3, e247 (2007).
    • (2007) PLOS Comput. Biol. , vol.3 , pp. e247
    • Zhu, J.1
  • 62
    • 40049091292 scopus 로고    scopus 로고
    • Using native and syntenically mapped cDNA alignments to improve de novo gene finding
    • Stanke, M., Diekhans, M., Baertsch, R., Haussler, D. Using native and syntenically mapped cDNA alignments to improve de novo gene finding. Bioinformatics 24, 637-644 (2008).
    • (2008) Bioinformatics , vol.24 , pp. 637-644
    • Stanke, M.1    Diekhans, M.2    Baertsch, R.3    Haussler, D.4
  • 63
    • 79952380591 scopus 로고    scopus 로고
    • Cactus graphs for genome comparisons
    • Paten, B., et al. Cactus graphs for genome comparisons. J. Comput. Biol. 18, 469-481 (2011).
    • (2011) J. Comput. Biol. , vol.18 , pp. 469-481
    • Paten, B.1
  • 65
    • 84930083227 scopus 로고    scopus 로고
    • Improved genome inference in the MHC using a population reference graph
    • Dilthey, A., Cox, C., Iqbal, Z., Nelson, M.R., McVean, G. Improved genome inference in the MHC using a population reference graph. Nat. Genet. 47, 682-688 (2015).
    • (2015) Nat. Genet. , vol.47 , pp. 682-688
    • Dilthey, A.1    Cox, C.2    Iqbal, Z.3    Nelson, M.R.4    McVean, G.5
  • 67
    • 77951770756 scopus 로고    scopus 로고
    • BEDTools: A flexible suite of utilities for comparing genomic features
    • Quinlan, A.R., Hall, I.M. BEDTools: A flexible suite of utilities for comparing genomic features. Bioinformatics 26, 841-842 (2010).
    • (2010) Bioinformatics , vol.26 , pp. 841-842
    • Quinlan, A.R.1    Hall, I.M.2
  • 68
    • 84866266717 scopus 로고    scopus 로고
    • Mapping single molecule sequencing reads using basic local alignment with successive refinement (BLASR): Application and theory
    • Chaisson, M.J., Tesler, G. Mapping single molecule sequencing reads using basic local alignment with successive refinement (BLASR): Application and theory. BMC Bioinformatics 13, 238 (2012).
    • (2012) BMC Bioinformatics , vol.13 , pp. 238
    • Chaisson, M.J.1    Tesler, G.2
  • 70
    • 85013157844 scopus 로고    scopus 로고
    • Mapping DNA methylation with high-throughput nanopore sequencing
    • Rand, A.C., et al. Mapping DNA methylation with high-throughput nanopore sequencing. Nat. Methods 14, 411-413 (2017).
    • (2017) Nat. Methods , vol.14 , pp. 411-413
    • Rand, A.C.1


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