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Annual Review of Animal Biosciences

Volume 7, 2019

New Approaches for Genome Assembly and Scaffolding

Abstract

Affordable, high-throughput DNA sequencing has accelerated the pace of genome assembly over the past decade. Genome assemblies from high-throughput, short-read sequencing, however, are often not as contiguous as the first generation of genome assemblies. Whereas early genome assembly projects were often aided by clone maps or other mapping data, many current assembly projects forego these scaffolding data and only assemble genomes into smaller segments. Recently, new technologies have been invented that allow chromosome-scale assembly at a lower cost and faster speed than traditional methods. Here, we give an overview of the problem of chromosome-scale assembly and traditional methods for tackling this problem. We then review new technologies for chromosome-scale assembly and recent genome projects that used these technologies to create highly contiguous genome assemblies at low cost.

Keyword(s): assembly, comparative genomics, genome, high-throughput sequencing, scaffolding
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/content/journals/10.1146/annurev-animal-020518-115344
2019-02-15
2024-04-20
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Literature Cited

  1. 1. 
    Adams MD, Celniker SE, Holt RA, Evans CA, Gocayne JD et al. 2000. The genome sequence of Drosophila melanogaster. . Science 287:2185–95
     [Google Scholar]
  2. 2. 
    Venter JC, Adams MD, Myers EW, Li PW, Mural RJ et al. 2001. The sequence of the human genome. Science 291:1304–51
     [Google Scholar]
  3. 3. 
    Waterston RH, Lindblad-Toh K, Birney E, Rogers J, Abril JF et al. 2002. Initial sequencing and comparative analysis of the mouse genome. Nature 420:520
     [Google Scholar]
  4. 4. 
    Sanger F, Nicklen S, Coulson AR 1977. DNA sequencing with chain-terminating inhibitors. PNAS 74:5463–67
     [Google Scholar]
  5. 5. 
    Margulies M, Egholm M, Altman WE, Attiya S, Bader JS et al. 2005. Genome sequencing in microfabricated high-density picolitre reactors. Nature 437:376–80
     [Google Scholar]
  6. 6. 
    McKernan KJ, Peckham HE, Costa GL, McLaughlin SF, Fu Y et al. 2009. Sequence and structural variation in a human genome uncovered by short-read, massively parallel ligation sequencing using two-base encoding. Genome Res 19:1527–41
     [Google Scholar]
  7. 7. 
    Rothberg JM, Hinz W, Rearick TM, Schultz J, Mileski W et al. 2011. An integrated semiconductor device enabling non-optical genome sequencing. Nature 475:348–52
     [Google Scholar]
  8. 8. 
    Bentley DR, Balasubramanian S, Swerdlow HP, Smith GP, Milton J et al. 2008. Accurate whole human genome sequencing using reversible terminator chemistry. Nature 456:53–59
     [Google Scholar]
  9. 9. 
    Wheeler DA, Srinivasan M, Egholm M, Shen Y, Chen L et al. 2008. The complete genome of an individual by massively parallel DNA sequencing. Nature 452:872–76
     [Google Scholar]
  10. 10. 
    Metzker ML 2010. Sequencing technologies—the next generation. Nat. Rev. Genet. 11:31
     [Google Scholar]
  11. 11. 
    Stein LD 2010. The case for cloud computing in genome informatics. Genome Biol 11:207
     [Google Scholar]
  12. 12. 
    Glenn TC 2011. Field guide to next-generation DNA sequencers. Mol. Ecol. Resour. 11:759–69
     [Google Scholar]
  13. 13. 
    Heather JM, Chain B 2016. The sequence of sequencers: the history of sequencing DNA. Genomics 107:1–8
     [Google Scholar]
  14. 14. 
    Suh A, Weber CC, Kehlmaier C, Braun EL, Green RE et al. 2014. Early Mesozoic coexistence of amniotes and Hepadnaviridae. PLOS Genet 10:e1004559
     [Google Scholar]
  15. 15. 
    Cahill JA, Heintzman PD, Harris K, Teasdale MD, Kapp J et al. 2018. Genomic evidence of widespread admixture from polar bears into brown bears during the last ice age. Mol. Biol. Evol. 35:1120–29
     [Google Scholar]
  16. 16. 
    Green RE, Krause J, Briggs AW, Maricic T, Stenzel U et al. 2010. A draft sequence of the Neandertal genome. Science 328:710–22
     [Google Scholar]
  17. 17. 
    Prüfer K, Racimo F, Patterson N, Jay F, Sankararaman S et al. 2014. The complete genome sequence of a Neanderthal from the Altai Mountains. Nature 505:43–49
     [Google Scholar]
  18. 18. 
    Prüfer K, de Filippo C, Grote S, Mafessoni F, Korlević P et al. 2017. A high-coverage Neandertal genome from Vindija Cave in Croatia. Science 358:655–58
     [Google Scholar]
  19. 19. 
    Lamichhaney S, Berglund J, Almén MS, Maqbool K, Grabherr M et al. 2015. Evolution of Darwin's finches and their beaks revealed by genome sequencing. Nature 518:371–75
     [Google Scholar]
  20. 20. 
    Brandvain Y, Kenney AM, Flagel L, Coop G, Sweigart AL 2014. Speciation and introgression between Mimulus nasutus and Mimulus guttatus. . PLOS Genet 10:e1004410
     [Google Scholar]
  21. 21. 
    Hsu PD, Lander ES, Zhang F 2014. Development and applications of CRISPR-Cas9 for genome engineering. Cell 157:1262–78
     [Google Scholar]
  22. 22. 
    Jinek M, Chylinski K, Fonfara I, Hauer M, Doudna JA, Charpentier E 2012. A programmable dual-RNA-guided DNA endonuclease in adaptive bacterial immunity. Science 337:816–21
     [Google Scholar]
  23. 23. 
    Shah AN, Davey CF, Whitebirch AC, Miller AC, Moens CB 2015. Rapid reverse genetic screening using CRISPR in zebrafish. Nat. Methods 12:535–40
     [Google Scholar]
  24. 24. 
    Gurumurthy CB, Grati M, Ohtsuka M, Schilit SLP, Quadros RM, Liu XZ 2016. CRISPR: a versatile tool for both forward and reverse genetics research. Hum. Genet. 135:971–76
     [Google Scholar]
  25. 25. 
    Schatz MC, Delcher AL, Salzberg SL 2010. Assembly of large genomes using second-generation sequencing. Genome Res 20:1165–73
     [Google Scholar]
  26. 26. 
    Ye L, Hillier LW, Minx P, Thane N, Locke DP et al. 2011. A vertebrate case study of the quality of assemblies derived from next-generation sequences. Genome Biol 12:R31
     [Google Scholar]
  27. 27. 
    Alkan C, Sajjadian S, Eichler EE 2011. Limitations of next-generation genome sequence assembly. Nat. Methods 8:61–65
     [Google Scholar]
  28. 28. 
    Lewin HA, Larkin DM, Pontius J, O'Brien SJ 2009. Every genome sequence needs a good map. Genome Res 19:1925–28
     [Google Scholar]
  29. 29. 
    Minoche AE, Dohm JC, Himmelbauer H 2011. Evaluation of genomic high-throughput sequencing data generated on Illumina HiSeq and genome analyzer systems. Genome Biol 12:R112
     [Google Scholar]
  30. 30. 
    Eid J, Fehr A, Gray J, Luong K, Lyle J et al. 2009. Real-time DNA sequencing from single polymerase molecules. Science 323:133–38
     [Google Scholar]
  31. 31. 
    Rhoads A, Au KF 2015. PacBio sequencing and its applications. Genom. Proteom. Bioinform. 13:278–89
     [Google Scholar]
  32. 32. 
    Jain M, Olsen HE, Paten B, Akeson M 2016. The Oxford Nanopore MinION: delivery of nanopore sequencing to the genomics community. Genome Biol 17:239
     [Google Scholar]
  33. 33. 
    Meyer M, Kircher M 2010. Illumina sequencing library preparation for highly multiplexed target capture and sequencing. Cold Spring Harb. Protoc. 2010:6pdb.prot5448
     [Google Scholar]
  34. 34. 
    Picelli S, Björklund AK, Reinius B, Sagasser S, Winberg G, Sandberg R 2014. Tn5 transposase and tagmentation procedures for massively scaled sequencing projects. Genome Res 24:2033–40
     [Google Scholar]
  35. 35. 
    Gansauge M-T, Gerber T, Glocke I, Korlevic P, Lippik L et al. 2017. Single-stranded DNA library preparation from highly degraded DNA using T4 DNA ligase. Nucleic Acids Res 45:e79
     [Google Scholar]
  36. 36. 
    Lu H, Giordano F, Ning Z 2016. Oxford Nanopore MinION sequencing and genome assembly. Genom. Proteom. Bioinform. 14:265–79
     [Google Scholar]
  37. 37. 
    Mayjonade B, Gouzy J, Donnadieu C, Pouilly N, Marande W et al. 2016. Extraction of high-molecular-weight genomic DNA for long-read sequencing of single molecules. Biotechniques 61:203–5
     [Google Scholar]
  38. 38. 
    Staden R 1979. A strategy of DNA sequencing employing computer programs. Nucleic Acids Res 6:2601–10
     [Google Scholar]
  39. 39. 
    Li Z, Chen Y, Mu D, Yuan J, Shi Y et al. 2012. Comparison of the two major classes of assembly algorithms: overlap-layout-consensus and de-Bruijn-graph. Brief. Funct. Genom. 11:25–37
     [Google Scholar]
  40. 40. 
    Compeau PEC, Pevzner PA, Tesler G 2011. How to apply de Bruijn graphs to genome assembly. Nat. Biotechnol. 29:987–91
     [Google Scholar]
  41. 41. 
    Simpson JT, Pop M 2015. The theory and practice of genome sequence assembly. Annu. Rev. Genom. Hum. Genet. 16:153–72
     [Google Scholar]
  42. 42. 
    Britten RJ, Kohne DE 1968. Repeated sequences in DNA. Science 161:529–40
     [Google Scholar]
  43. 43. 
    Treangen TJ, Salzberg SL 2012. Repetitive DNA and next-generation sequencing: computational challenges and solutions. Nat. Rev. Genet. 13:36–46
     [Google Scholar]
  44. 44. 
    Kim J, Farre M, Auvil L, Capitanu B, Larkin DM et al. 2017. Reconstruction and evolutionary history of eutherian chromosomes. PNAS 114:E5379–88
     [Google Scholar]
  45. 45. 
    Larkin DM, Pape G, Donthu R, Auvil L, Welge M, Lewin HA 2009. Breakpoint regions and homologous synteny blocks in chromosomes have different evolutionary histories. Genome Res 19:770–77
     [Google Scholar]
  46. 46. 
    Sagai T, Hosoya M, Mizushina Y, Tamura M, Shiroishi T 2005. Elimination of a long-range cis-regulatory module causes complete loss of limb-specific Shh expression and truncation of the mouse limb. Development 132:797–803
     [Google Scholar]
  47. 47. 
    Maston GA, Evans SK, Green MR 2006. Transcriptional regulatory elements in the human genome. Annu. Rev. Genom. Hum. Genet. 7:29–59
     [Google Scholar]
  48. 48. 
    Pombo A, Dillon N 2015. Three-dimensional genome architecture: players and mechanisms. Nat. Rev. Mol. Cell Biol. 16:245–57
     [Google Scholar]
  49. 49. 
    Batugedara G, Lu XM, Bunnik EM, Le Roch KG 2017. The role of chromatin structure in gene regulation of the human malaria parasite. Trends Parasitol 33:364–77
     [Google Scholar]
  50. 50. 
    Rice ES, Kohno S, John JS, Pham S, Howard J et al. 2017. Improved genome assembly of American alligator genome reveals conserved architecture of estrogen signaling. Genome Res 27:686–96
     [Google Scholar]
  51. 51. 
    Jensen-Seaman MI, Furey TS, Payseur BA, Lu Y, Roskin KM et al. 2004. Comparative recombination rates in the rat, mouse, and human genomes. Genome Res 14:528–38
     [Google Scholar]
  52. 52. 
    Backström N, Forstmeier W, Schielzeth H, Mellenius H, Nam K et al. 2010. The recombination landscape of the zebra finch Taeniopygia guttata genome. Genome Res 20:485–95
     [Google Scholar]
  53. 53. 
    Lichten M, Goldman ASH 1995. Meiotic recombination hotspots. Annu. Rev. Genet. 29:423–44
     [Google Scholar]
  54. 54. 
    Ellegren H 2010. Evolutionary stasis: the stable chromosomes of birds. Trends Ecol. Evol. 25:283–91
     [Google Scholar]
  55. 55. 
    Murray GGR, Soares AER, Novak BJ, Schaefer NK, Cahill JA et al. 2017. Natural selection shaped the rise and fall of passenger pigeon genomic diversity. Science 358:951–54
     [Google Scholar]
  56. 56. 
    Lewis CM, Knight J 2012. Introduction to genetic association studies. Cold Spring Harb. Protoc. 2012:3297–306
     [Google Scholar]
  57. 57. 
    Lohmueller KE, Pearce CL, Pike M, Lander ES, Hirschhorn JN 2003. Meta-analysis of genetic association studies supports a contribution of common variants to susceptibility to common disease. Nat. Genet. 33:177
     [Google Scholar]
  58. 58. 
    Iles MM 2008. What can genome-wide association studies tell us about the genetics of common disease?. PLOS Genet 4:e33
     [Google Scholar]
  59. 59. 
    Chang D, Nalls MA, Hallgrímsdóttir IB, Hunkapiller J, van der Brug M et al. 2017. A meta-analysis of genome-wide association studies identifies 17 new Parkinson's disease risk loci. Nat. Genet. 49:1511–16
     [Google Scholar]
  60. 60. 
    Lee JC, Biasci D, Roberts R, Gearry RB, Mansfield JC et al. 2017. Genome-wide association study identifies distinct genetic contributions to prognosis and susceptibility in Crohn's disease. Nat. Genet. 49:262–68
     [Google Scholar]
  61. 61. 
    Parchman TL, Gompert Z, Mudge J, Schilkey FD, Benkman CW, Buerkle CA 2012. Genome-wide association genetics of an adaptive trait in lodgepole pine. Mol. Ecol. 21:2991–3005
     [Google Scholar]
  62. 62. 
    Cai Q, Qian X, Lang Y, Luo Y, Xu J et al. 2013. Genome sequence of ground tit Pseudopodoces humilis and its adaptation to high altitude. Genome Biol 14:R29
     [Google Scholar]
  63. 63. 
    Cohen MM, Gans C 1970. The chromosomes of the order Crocodilia. Cytogenetics 9:81–105
     [Google Scholar]
  64. 64. 
    Srikulnath K, Thapana W, Muangmai N 2015. Role of chromosome changes in Crocodylus evolution and diversity. Genom. Inform. 13:102–11
     [Google Scholar]
  65. 65. 
    Murphy WJ, Larkin DM, Everts-van der Wind A, Bourque G, Tesler G et al. 2005. Dynamics of mammalian chromosome evolution inferred from multispecies comparative maps. Science 309:613–17
     [Google Scholar]
  66. 66. 
    Graphodatsky AS, Trifonov VA, Stanyon R 2011. The genome diversity and karyotype evolution of mammals. Mol. Cytogenet. 4:22
     [Google Scholar]
  67. 67. 
    Perelman P, Johnson WE, Roos C, Seuánez HN, Horvath JE et al. 2011. A molecular phylogeny of living primates. PLOS Genet 7:e1001342
     [Google Scholar]
  68. 68. 
    Noor MAF, Grams KL, Bertucci LA, Reiland J 2001. Chromosomal inversions and the reproductive isolation of species. PNAS 98:12084–88
     [Google Scholar]
  69. 69. 
    Walsh JB 1982. Rate of accumulation of reproductive isolation by chromosome rearrangements. Am. Nat. 120:510–32
     [Google Scholar]
  70. 70. 
    Abbott JK, Nordén AK, Hansson B 2017. Sex chromosome evolution: historical insights and future perspectives. Proc. R. Soc. B 284:20162806
     [Google Scholar]
  71. 71. 
    Salse J, Abrouk M, Bolot S, Guilhot N, Courcelle E et al. 2009. Reconstruction of monocotelydoneous proto-chromosomes reveals faster evolution in plants than in animals. PNAS 106:14908–13
     [Google Scholar]
  72. 72. 
    Murat F, Zhang R, Guizard S, Gavranović H, Flores R et al. 2015. Karyotype and gene order evolution from reconstructed extinct ancestors highlight contrasts in genome plasticity of modern rosid crops. Genome Biol. Evol. 7:735–49
     [Google Scholar]
  73. 73. 
    O'Connor RE, Romanov MN, Kiazim LG, Barrett PM, Farré M et al. 2018. Reconstruction of the diapsid ancestral genome permits chromosome evolution tracing in avian and non-avian dinosaurs. Nat. Commun. 9:1883
     [Google Scholar]
  74. 74. 
    Morgan TH 1911. Random segregation versus coupling in Mendelian inheritance. Science 34:384
     [Google Scholar]
  75. 75. 
    Sturtevant AH 1913. The linear arrangement of six sex-linked factors in Drosophila, as shown by their mode of association. J. Exp. Zool. 14:43–59
     [Google Scholar]
  76. 76. 
    Mascher M, Stein N 2014. Genetic anchoring of whole-genome shotgun assemblies. Front. Genet. 5:208
     [Google Scholar]
  77. 77. 
    Fierst JL 2015. Using linkage maps to correct and scaffold de novo genome assemblies: methods, challenges, and computational tools. Front. Genet. 6:220
     [Google Scholar]
  78. 78. 
    Deleted in proof
  79. 79. 
    Nossa CW, Havlak P, Yue J-X, Lv J, Vincent KY et al. 2014. Joint assembly and genetic mapping of the Atlantic horseshoe crab genome reveals ancient whole genome duplication. Gigascience 3:9
     [Google Scholar]
  80. 80. 
    Kai W, Kikuchi K, Tohari S, Chew AK, Tay A et al. 2011. Integration of the genetic map and genome assembly of fugu facilitates insights into distinct features of genome evolution in teleosts and mammals. Genome Biol. Evol. 3:424–42
     [Google Scholar]
  81. 81. 
    Goss SJ, Harris H 1975. New method for mapping genes in human chromosomes. Nature 255:680
     [Google Scholar]
  82. 82. 
    Cox DR, Burmeister M, Price ER, Kim S, Myers RM 1990. Radiation hybrid mapping: a somatic cell genetic method for constructing high-resolution maps of mammalian chromosomes. Science 250:245–50
     [Google Scholar]
  83. 83. 
    Deloukas P 2005. Radiation hybrid mapping. eLS https://doi.org/10.1038/npg.els.0005361
    [Crossref]
  84. 84. 
    Kumar A, Bassi FM, Paux E, Al-Azzam O, de Jimenez MM et al. 2012. DNA repair and crossing over favor similar chromosome regions as discovered in radiation hybrid of Triticum. . BMC Genom 13:339
     [Google Scholar]
  85. 85. 
    Yang Y-P, Womack JE 1998. Parallel radiation hybrid mapping: a powerful tool for high-resolution genomic comparison. Genome Res 8:731–36
     [Google Scholar]
  86. 86. 
    Howe K, Clark MD, Torroja CF, Torrance J, Berthelot C et al. 2013. The zebrafish reference genome sequence and its relationship to the human genome. Nature 496:498
     [Google Scholar]
  87. 87. 
    Bickhart DM, Rosen BD, Koren S, Sayre BL, Hastie AR et al. 2017. Single-molecule sequencing and chromatin conformation capture enable de novo reference assembly of the domestic goat genome. Nat. Genet. 49:643
     [Google Scholar]
  88. 88. 
    Warren WC, Hillier LW, Tomlinson C, Minx P, Kremitzki M et al. 2017. A new chicken genome assembly provides insight into avian genome structure. G3 Genes Genomes Genet 7:109–17
     [Google Scholar]
  89. 89. 
    Kalbfleisch TS, Rice ES, DePriest MS Jr., Walenz BP, Hestand MS et al. 2018. Improved reference genome for the domestic horse increases assembly contiguity and composition. Commun. Biol 1:197
     [Google Scholar]
  90. 90. 
    Espinosa R, Le Beau MM 2000. Gene mapping by FISH. The Nucleic Acid Protocols Handbook R Rapley 991–1010 New York: Springer
     [Google Scholar]
  91. 91. 
    Speicher MR, Ballard SG, Ward DC 1996. Karyotyping human chromosomes by combinatorial multi-fluor FISH. Nat. Genet. 12:368
     [Google Scholar]
  92. 92. 
    Schröck E, Du Manoir S, Veldman T, Schoell B, Wienberg J et al. 1996. Multicolor spectral karyotyping of human chromosomes. Science 273:494–97
     [Google Scholar]
  93. 93. 
    Fan Y-S, Davis LM, Shows TB 1990. Mapping small DNA sequences by fluorescence in situ hybridization directly on banded metaphase chromosomes. PNAS 87:6223–27
     [Google Scholar]
  94. 94. 
    Trask B, Pinkel D, van den Engh G 1989. The proximity of DNA sequences in interphase cell nuclei is correlated to genomic distance and permits ordering of cosmids spanning 250 kilobase pairs. Genomics 5:710–17
     [Google Scholar]
  95. 95. 
    Raap AK, Florijn RJ, Blonden LAJ, Wiegant J, Vaandrager J-W et al. 1996. Fiber FISH as a DNA mapping tool. Methods 9:67–73
     [Google Scholar]
  96. 96. 
    Shearer LA, Anderson LK, De Jong H, Smit S, Goicoechea JL et al. 2014. Fluorescence in situ hybridization and optical mapping to correct scaffold arrangement in the tomato genome. G3 Genes Genomes Genet 4:1395–405
     [Google Scholar]
  97. 97. 
    Vij S, Kuhl H, Kuznetsova IS, Komissarov A, Yurchenko AA et al. 2016. Chromosomal-level assembly of the Asian seabass genome using long sequence reads and multi-layered scaffolding. PLOS Genet 12:e1005954
     [Google Scholar]
  98. 98. 
    O'Connor M, Peifer M, Bender W 1989. Construction of large DNA segments in Escherichia coli. . Science 244:1307–12
     [Google Scholar]
  99. 99. 
    Kelley JM, Field CE, Craven MB, Rounsley SD, Adams MD et al. 1999. High throughput direct end sequencing of BAC clones. Nucleic Acids Res 27:1539–46
     [Google Scholar]
  100. 100. 
    Han CS, Sutherland RD, Jewett PB, Campbell ML, Meincke LJ et al. 2000. Construction of a BAC contig map of chromosome 16q by two-dimensional overgo hybridization. Genome Res 10:714–21
     [Google Scholar]
  101. 101. 
    Ardui S, Ameur A, Vermeesch JR, Hestand MS 2018. Single molecule real-time (SMRT) sequencing comes of age: applications and utilities for medical diagnostics. Nucleic Acids Res 46:2159–68
     [Google Scholar]
  102. 102. 
    Levene MJ, Korlach J, Turner SW, Foquet M, Craighead HG, Webb WW 2003. Zero-mode waveguides for single-molecule analysis at high concentrations. Science 299:682–86
     [Google Scholar]
  103. 103. 
    Chin C-S, Peluso P, Sedlazeck FJ, Nattestad M, Concepcion GT et al. 2016. Phased diploid genome assembly with single-molecule real-time sequencing. Nat. Methods 13:1050–54
     [Google Scholar]
  104. 104. 
    Ritz A, Bashir A, Sindi S, Hsu D, Hajirasouliha I, Raphael BJ 2014. Characterization of structural variants with single molecule and hybrid sequencing approaches. Bioinformatics 30:3458–66
     [Google Scholar]
  105. 105. 
    Feng Y, Zhang Y, Ying C, Wang D, Du C 2015. Nanopore-based fourth-generation DNA sequencing technology. Genom. Proteom. Bioinform. 13:4–16
     [Google Scholar]
  106. 106. 
    Cherf GM, Lieberman KR, Rashid H, Lam CE, Karplus K, Akeson M 2012. Automated forward and reverse ratcheting of DNA in a nanopore at 5-Å precision. Nat. Biotechnol. 30:344–48
     [Google Scholar]
  107. 107. 
    Jain M, Koren S, Miga KH, Quick J, Rand AC et al. 2018. Nanopore sequencing and assembly of a human genome with ultra-long reads. Nat. Biotechnol. 36:338–45
     [Google Scholar]
  108. 108. 
    Payne A, Holmes N, Rakyan V, Loose M 2018. Whale watching with BulkVis: a graphical viewer for Oxford Nanopore bulk fast5 files. bioRxiv 312256. https://doi.org/10.1101/312256
    [Crossref]
  109. 109. 
    Laver T, Harrison J, O'Neill PA, Moore K, Farbos A et al. 2015. Assessing the performance of the Oxford Nanopore Technologies MinION. Biomol. Detect. Quantif. 3:1–8
     [Google Scholar]
  110. 110. 
    Wick RR, Judd LM, Holt KE 2018. Comparison of Oxford Nanopore basecalling tools. https://doi.org/10.5281/zenodo.1188469
    [Crossref]
  111. 111. 
    Madoui M-A, Engelen S, Cruaud C, Belser C, Bertrand L et al. 2015. Genome assembly using Nanopore-guided long and error-free DNA reads. BMC Genom 16:327
     [Google Scholar]
  112. 112. 
    Sović I, Križanović K, Skala K, Šikić M 2016. Evaluation of hybrid and non-hybrid methods for de novo assembly of nanopore reads. Bioinformatics 32:2582–89
     [Google Scholar]
  113. 113. 
    Tyson JR, O'Neil NJ, Jain M, Olsen HE, Hieter P, Snutch TP 2018. MinION-based long-read sequencing and assembly extends the Caenorhabditis elegans reference genome. Genome Res 28:266–74
     [Google Scholar]
  114. 114. 
    Giordano F, Aigrain L, Quail MA, Coupland P, Bonfield JK et al. 2017. De novo yeast genome assemblies from MinION, PacBio and MiSeq platforms. Sci. Rep. 7:3935
     [Google Scholar]
  115. 115. 
    Loman NJ, Quick J, Simpson JT 2015. A complete bacterial genome assembled de novo using only nanopore sequencing data. Nat. Methods 12:733–35
     [Google Scholar]
  116. 116. 
    Li C, Chng KR, Boey EJH, Ng AHQ, Wilm A, Nagarajan N 2016. INC-Seq: accurate single molecule reads using nanopore sequencing. Gigascience 5:34
     [Google Scholar]
  117. 117. 
    Ekblom R, Wolf JBW 2014. A field guide to whole-genome sequencing, assembly and annotation. Evol. Appl. 7:1026–42
     [Google Scholar]
  118. 118. 
    Koren S, Schatz MC, Walenz BP, Martin J, Howard JT et al. 2012. Hybrid error correction and de novo assembly of single-molecule sequencing reads. Nat. Biotechnol. 30:693–700
     [Google Scholar]
  119. 119. 
    Myers EW, Sutton GG, Delcher AL, Dew IM, Fasulo DP et al. 2000. A whole-genome assembly of Drosophila. . Science 287:2196–204
     [Google Scholar]
  120. 120. 
    Lee H, Gurtowski J, Yoo S, Marcus S, McCombie WR, Schatz M 2014. Error correction and assembly complexity of single molecule sequencing reads. bioRxiv 006395. https://doi.org/10.1101/006395
    [Crossref]
  121. 121. 
    Kurtz S, Phillippy A, Delcher AL, Smoot M, Shumway M et al. 2004. Versatile and open software for comparing large genomes. Genome Biol 5:R12
     [Google Scholar]
  122. 122. 
    Bankevich A, Nurk S, Antipov D, Gurevich AA, Dvorkin M et al. 2012. SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing. J. Comput. Biol. 19:455–77
     [Google Scholar]
  123. 123. 
    Ye C, Hill CM, Wu S, Ruan J, Ma Z 2016. DBG2OLC: efficient assembly of large genomes using long erroneous reads of the third generation sequencing technologies. Sci. Rep. 6:31900
     [Google Scholar]
  124. 124. 
    Chin C-S, Alexander DH, Marks P, Klammer AA, Drake J et al. 2013. Nonhybrid, finished microbial genome assemblies from long-read SMRT sequencing data. Nat. Methods 10:563
     [Google Scholar]
  125. 125. 
    Koren S, Walenz BP, Berlin K, Miller JR, Bergman NH, Phillippy AM 2017. Canu: scalable and accurate long-read assembly via adaptive k-mer weighting and repeat separation. Genome Res 27:722–36
     [Google Scholar]
  126. 126. 
    Berlin K, Koren S, Chin C-S, Drake JP, Landolin JM, Phillippy AM 2015. Assembling large genomes with single-molecule sequencing and locality-sensitive hashing. Nat. Biotechnol. 33:623–30
     [Google Scholar]
  127. 127. 
    Miller JR, Delcher AL, Koren S, Venter E, Walenz BP et al. 2008. Aggressive assembly of pyrosequencing reads with mates. Bioinformatics 24:2818–24
     [Google Scholar]
  128. 128. 
    Li H 2016. Minimap and miniasm: fast mapping and de novo assembly for noisy long sequences. Bioinformatics 32:2103–10
     [Google Scholar]
  129. 129. 
    Kolmogorov M, Yuan J, Lin Y, Pevzner P 2018. Assembly of long error-prone reads using repeat graphs. bioRxiv 247148. https://doi.org/10.1101/247148
    [Crossref]
  130. 130. 
    Lin Y, Yuan J, Kolmogorov M, Shen MW, Chaisson M, Pevzner PA 2016. Assembly of long error-prone reads using de Bruijn graphs. PNAS 113:E8396–E405
     [Google Scholar]
  131. 131. 
    English AC, Richards S, Han Y, Wang M, Vee V et al. 2012. Mind the gap: upgrading genomes with Pacific Biosciences RS long-read sequencing technology. PLOS ONE 7:e47768
     [Google Scholar]
  132. 132. 
    Warren RL, Yang C, Vandervalk BP, Behsaz B, Lagman A et al. 2015. LINKS: scalable, alignment-free scaffolding of draft genomes with long reads. Gigascience 4:35
     [Google Scholar]
  133. 133. 
    Walker BJ, Abeel T, Shea T, Priest M, Abouelliel A et al. 2014. Pilon: an integrated tool for comprehensive microbial variant detection and genome assembly improvement. PLOS ONE 9:e112963
     [Google Scholar]
  134. 134. 
    de Wit E, de Laat W 2012. A decade of 3C technologies: insights into nuclear organization. Genes Dev 26:11–24
     [Google Scholar]
  135. 135. 
    Dekker J, Rippe K, Dekker M, Kleckner N 2002. Capturing chromosome conformation. Science 295:1306–11
     [Google Scholar]
  136. 136. 
    Lieberman-Aiden E, van Berkum NL, Williams L, Imakaev M, Ragoczy T et al. 2009. Comprehensive mapping of long-range interactions reveals folding principles of the human genome. Science 326:289–93
     [Google Scholar]
  137. 137. 
    Burton JN, Adey A, Patwardhan RP, Qiu R, Kitzman JO, Shendure J 2013. Chromosome-scale scaffolding of de novo genome assemblies based on chromatin interactions. Nat. Biotechnol. 31:1119–25
     [Google Scholar]
  138. 138. 
    Putnam NH, O'Connell BL, Stites JC, Rice BJ, Blanchette M et al. 2016. Chromosome-scale shotgun assembly using an in vitro method for long-range linkage. Genome Res 26:342–50
     [Google Scholar]
  139. 139. 
    Kaplan N, Dekker J 2013. High-throughput genome scaffolding from in vivo DNA interaction frequency. Nat. Biotechnol. 31:1143
     [Google Scholar]
  140. 140. 
    Korbel JO, Lee C 2013. Genome assembly and haplotyping with Hi-C. Nat. Biotechnol. 31:1099
     [Google Scholar]
  141. 141. 
    Dudchenko O, Batra SS, Omer AD, Nyquist SK, Hoeger M et al. 2017. De novo assembly of the Aedes aegypti genome using Hi-C yields chromosome-length scaffolds. Science 356:92–95
     [Google Scholar]
  142. 142. 
    Dudchenko O, Shamim MS, Batra S, Durand NC, Musial NT et al. 2018. The Juicebox Assembly Tools module facilitates de novo assembly of mammalian genomes with chromosome-length scaffolds for under $1000. bioRxiv 254797. https://doi.org/10.1101/254797
    [Crossref]
  143. 143. 
    Ghurye J, Pop M, Koren S, Bickhart D, Chin C-S 2017. Scaffolding of long read assemblies using long range contact information. BMC Genom 18:527
     [Google Scholar]
  144. 144. 
    Ghurye J, Rhie A, Walenz BP, Schmitt A, Selvaraj S et al. 2018. Integrating Hi-C links with assembly graphs for chromosome-scale assembly. bioRxiv 261149. https://doi.org/10.1101/261149
    [Crossref]
  145. 145. 
    Amini S, Pushkarev D, Christiansen L, Kostem E, Royce T et al. 2014. Haplotype-resolved whole-genome sequencing by contiguity-preserving transposition and combinatorial indexing. Nat. Genet. 46:1343–49
     [Google Scholar]
  146. 146. 
    Adey A, Kitzman JO, Burton JN, Daza R, Kumar A et al. 2014. In vitro, long-range sequence information for de novo genome assembly via transposase contiguity. Genome Res 24:2041–49
     [Google Scholar]
  147. 147. 
    Zheng GXY, Lau BT, Schnall-Levin M, Jarosz M, Bell JM et al. 2016. Haplotyping germline and cancer genomes with high-throughput linked-read sequencing. Nat. Biotechnol. 34:303–11
     [Google Scholar]
  148. 148. 
    Garcia S, Williams S, Xu AW, Herschleb J, Marks P et al. 2017. Linked-read sequencing resolves complex structural variants. bioRxiv 231662. https://doi.org/10.1101/231662
    [Crossref]
  149. 149. 
    Weisenfeld NI, Kumar V, Shah P, Church DM, Jaffe DB 2017. Direct determination of diploid genome sequences. Genome Res 27:757–67
     [Google Scholar]
  150. 150. 
    Mak ACY, Lai YYY, Lam ET, Kwok T-P, Leung AKY et al. 2016. Genome-wide structural variation detection by genome mapping on nanochannel arrays. Genetics 202:351–62
     [Google Scholar]
  151. 151. 
    Cao H, Hastie AR, Cao D, Lam ET, Sun Y et al. 2014. Rapid detection of structural variation in a human genome using nanochannel-based genome mapping technology. Gigascience 3:34
     [Google Scholar]
  152. 152. 
    Shi L, Guo Y, Dong C, Huddleston J, Yang H et al. 2016. Long-read sequencing and de novo assembly of a Chinese genome. Nat. Commun. 7:12065
     [Google Scholar]
  153. 153. 
    Seo J-S, Rhie A, Kim J, Lee S, Sohn M-H et al. 2016. De novo assembly and phasing of a Korean human genome. Nature 538:243–47
     [Google Scholar]
  154. 154. 
    Dong Y, Xie M, Jiang Y, Xiao N, Du X et al. 2013. Sequencing and automated whole-genome optical mapping of the genome of a domestic goat (Capra hircus). Nat. Biotechnol. 31:135–41
     [Google Scholar]
  155. 155. 
    Kolmogorov M, Raney B, Paten B, Pham S 2014. Ragout—a reference-assisted assembly tool for bacterial genomes. Bioinformatics 30:i302–9
     [Google Scholar]
  156. 156. 
    Yuan L, Yu Y, Zhu Y, Li Y, Li C et al. 2017. GAAP: Genome-organization-framework-Assisted Assembly Pipeline for prokaryotic genomes. BMC Genom 18:952
     [Google Scholar]
  157. 157. 
    Kim J, Larkin DM, Cai Q, Zhang Y, Ge R-L et al. 2013. Reference-assisted chromosome assembly. PNAS 110:1785–90
     [Google Scholar]
  158. 158. 
    Kolmogorov M, Armstrong J, Raney BJ, Streeter I, Dunn M et al. 2018. Chromosome assembly of large and complex genomes using multiple references. Genome Res 28:1720–32
     [Google Scholar]
  159. 159. 
    Murphy WJ, Larkin DM, Everts-van der Wind A, Bourque G, Tesler G et al. 2005. Dynamics of mammalian chromosome evolution inferred from multispecies comparative maps. Science 309:613–17
     [Google Scholar]
  160. 160. 
    Glusman G, Cox HC, Roach JC 2014. Whole-genome haplotyping approaches and genomic medicine. Genome Med 6:73
     [Google Scholar]
  161. 161. 
    Koren S, Rhie A, Walenz BP, Dilthey AT, Bickhart DM et al. 2018. De novo assembly of haplotype-resolved genomes with trio binning. Nat. Biotechnol. 36:1174–82
     [Google Scholar]
  162. 162. 
    Gordon D, Huddleston J, Chaisson MJP, Hill CM, Kronenberg ZN et al. 2016. Long-read sequence assembly of the gorilla genome. Science 352:aae0344
     [Google Scholar]
  163. 163. 
    Larsen PA, Harris RA, Liu Y, Murali SC, Campbell CR et al. 2017. Hybrid de novo genome assembly and centromere characterization of the gray mouse lemur (Microcebus murinus). BMC Biol 15:110
     [Google Scholar]
  164. 164. 
    Kuderna LFK, Tomlinson C, Hillier LW, Tran A, Fiddes IT et al. 2017. A 3-way hybrid approach to generate a new high-quality chimpanzee reference genome (Pan_tro_3.0). Gigascience 6:1–6
     [Google Scholar]
  165. 165. 
    Thybert D, Roller M, Navarro FCP, Fiddes I, Streeter I et al. 2018. Repeat associated mechanisms of genome evolution and function revealed by the Mus caroli and Mus pahari genomes. Genome Res 28:448–59
     [Google Scholar]
  166. 166. 
    Hammond SA, Warren RL, Vandervalk BP, Kucuk E, Khan H et al. 2017. The North American bullfrog draft genome provides insight into hormonal regulation of long noncoding RNA. Nat. Commun. 8:1433
     [Google Scholar]
  167. 167. 
    Jones SJM, Taylor GA, Chan S, Warren RL, Hammond SA et al. 2017. The genome of the beluga whale (Delphinapterus leucas). Genes 8:378
     [Google Scholar]
  168. 168. 
    Zerbino DR, Birney E 2008. Velvet: algorithms for de novo short read assembly using de Bruijn graphs. Genome Res 18:821–29
     [Google Scholar]
  169. 169. 
    Luo R, Liu B, Xie Y, Li Z, Huang W et al. 2012. SOAPdenovo2: an empirically improved memory-efficient short-read de novo assembler. Gigascience 1:18
     [Google Scholar]
  170. 170. 
    Chapman JA, Ho I, Sunkara S, Luo S, Schroth GP, Rokhsar DS 2011. Meraculous: de novo genome assembly with short paired-end reads. PLOS ONE 6:e23501
     [Google Scholar]
  171. 171. 
    Gnerre S, MacCallum I, Przybylski D, Ribeiro FJ, Burton JN et al. 2011. High-quality draft assemblies of mammalian genomes from massively parallel sequence data. PNAS 108:1513–18
     [Google Scholar]
  172. 172. 
    Simpson JT, Durbin R 2012. Efficient de novo assembly of large genomes using compressed data structures. Genome Res 22:549–56
     [Google Scholar]
  173. 173. 
    Jackman SD, Vandervalk BP, Mohamadi H, Chu J, Yeo S et al. 2017. ABySS 2.0: resource-efficient assembly of large genomes using a Bloom filter. Genome Res 27:768–77
     [Google Scholar]
  174. 174. 
    Love RR, Weisenfeld NI, Jaffe DB, Besansky NJ, Neafsey DE 2016. Evaluation of DISCOVAR de novo using a mosquito sample for cost-effective short-read genome assembly. BMC Genom 17:187
     [Google Scholar]
  175. 175. 
    Jarvis ED, Mirarab S, Aberer AJ, Li B, Houde P et al. 2014. Whole-genome analyses resolve early branches in the tree of life of modern birds. Science 346:1320–31
     [Google Scholar]
  176. 176. 
    Gordon D, Huddleston J, Chaisson MJ, Hill CM, Kronenberg ZN et al. 2016. Long-read sequence assembly of the gorilla genome. Science 352:aae0344
     [Google Scholar]
/content/journals/10.1146/annurev-animal-020518-115344
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New Approaches for Genome Assembly and Scaffolding
Annual Review of Animal Biosciences 7, 17 (2019); https://doi.org/10.1146/annurev-animal-020518-115344
/content/journals/10.1146/annurev-animal-020518-115344
/content/journals/10.1146/annurev-animal-020518-115344
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