[1] Maxam AM, Gilbert W. A new method for sequencing DNA. Proc Natl Acad Sci USA , 1977, 74(2): 560-564. [2] Sanger F, Nicklen S, Coulson AR. DNA sequencing with chain-terminating inhibitors. Proc Natl Acad Sci USA , 1977, 74(12): 5463-5467. [3] Liu L, Li YH, Li SL, Hu N, He YM, Pong R, Lin DN, Lu LH, Law M. Comparison of next-generation sequencing systems. J Biomed Biotechnol , 2012, 2012: Article ID 251364. [4] Gilles A, Meglécz E, Pech N, Ferreira S, Malausa T, Martin JF. Accuracy and quality assessment of 454 GS-FLX Titanium pyrosequencing. BMC Genom , 2011, 12(1): 245. [5] Chin CS, Sorenson J, Harris JB, Robins WP, Charles RC, Jean-Charles RR, Bullard J, Webster DR, Kasarskis A, Peluso P, Paxinos EE, Yamaichi Y, Calderwood SB, Mekalanos JJ, Schadt EE, Waldor MK. The origin of the Haitian cholera outbreak strain. N Engl J Med , 2011, 364(1): 33-42. [6] Rasko DA, Webster DR, Sahl JW, Bashir A, Boisen N, Scheutz F, Paxinos EE, Sebra R, Chin CS, Iliopoulos D, Klammer A, Peluso P, Lee L, Kislyuk AO, Bullard J, Kasarskis A, Wang S, Eid J, Rank D, Redman JC, Steyert SR, Frimodt-Møller J, Struve C, Petersen AM, Krogfelt KA, Nataro JP, Schadt EE, Waldor MK. Origins of the E. coli strain causing an outbreak of hemolytic-uremic syndrome in Germany. N Engl J Med , 2011, 365(8): 709-717. [7] Margulies M, Egholm M, Altman WE, Attiya S, Bader JS, Bemben LA, Berka J, Braverman MS, Chen YJ, Chen ZT, Dewell SB, Du L, Fierro JM, Gomes XV, Godwin BC, He W, Helgesen S, Ho CH, Irzyk GP, Jando SC, Alenquer ML, Jarvie TP, Jirage KB, Kim JB, Knight JR, Lanza JR, Leamon JH, Lefkowitz SM, Lei M, Li J, Lohman KL, Lu H, Makhijani VB, McDade KE, McKenna MP, Myers EW, Nickerson E, Nobile JR, Plant R, Puc BP, Ronan MT, Roth GT, Sarkis GJ, Simons JF, Simpson JW, Srinivasan M, Tartaro KR, Tomasz A, Vogt KA, Volkmer GA, Wang SH, Wang Y, Weiner MP, Yu PG, Begley RF, Rothberg JM. Genome sequencing in microfabricated high-density picolitre reactors. Nature , 2005, 437(7057): 376-380. [8] Bentley DR, Balasubramanian S, Swerdlow HP, Smith GP, Milton J, Brown CG, Hall KP, Evers DJ, Barnes CL, Bignell HR, Boutell JM, Bryant J, Carter RJ, Keira Cheetham R, Cox AJ, Ellis DJ, Flatbush MR, Gormley NA, Humphray SJ, Irving LJ, Karbelashvili MS, Kirk SM, Li H, Liu XH, Maisinger KS, Murray LJ, Obradovic B, Ost T, Parkinson ML, Pratt MR, Rasolonjatovo IM, Reed MT, Rigatti R, Rodighiero C, Ross MT, Sabot A, Sankar SV, Scally A, Schroth GP, Smith ME, Smith VP, Spiridou A, Torrance PE, Tzonev SS, Vermaas EH, Walter K, Wu XL, Zhang L, Alam MD, Anastasi C, Aniebo IC, Bailey DM, Bancarz IR, Banerjee S, Barbour SG, Baybayan PA, Benoit VA, Benson KF, Bevis C, Black PJ, Boodhun A, Brennan JS, Bridgham JA, Brown RC, Brown AA, Buermann DH, Bundu AA, Burrows JC, Carter NP, Castillo N, Chiara E Catenazzi M, Chang S, Neil Cooley R, Crake NR, Dada OO, Diakoumakos KD, Dominguez-Fernandez B, Earnshaw DJ, Egbujor UC, Elmore DW, Etchin SS, Ewan MR, Fedurco M, Fraser LJ, Fuentes Fajardo KV, Scott Furey W, George D, Gietzen KJ, Goddard CP, Golda GS, Granieri PA, Green DE, Gustafson DL, Hansen NF, Harnish K, Haudenschild CD, Heyer NI, Hims MM, Ho JT, Horgan AM, Hoschler K, Hurwitz S, Ivanov DV, Johnson MQ, James T, Huw Jones TA, Kang GD, Kerelska TH, Kersey AD, Khrebtukova I, Kindwall AP, Kingsbury Z, Kokko-Gonzales PI, Kumar A, Laurent MA, Lawley CT, Lee SE, Lee X, Liao AK, Loch JA, Lok M, Luo SJ, Mammen RM, Martin JW, McCauley PG, McNitt P, Mehta P, Moon KW, Mullens JW, Newington T, Ning ZM, Ling Ng B, Novo SM, O'Neill MJ, Osborne MA, Osnowski A, Ostadan O, Paraschos LL, Pickering L, Pike AC, Pike AC, Chris Pinkard D, Pliskin DP, Podhasky J, Quijano VJ, Raczy C, Rae VH, Rawlings SR, Chiva Rodriguez A, Roe PM, Rogers J, Rogert Bacigalupo MC, Romanov N, Romieu A, Roth RK, Rourke NJ, Ruediger ST, Rusman E, Sanches-Kuiper RM, Schenker MR, Seoane JM, Shaw RJ, Shiver MK, Short SW, Sizto NL, Sluis JP, Smith MA, Ernest Sohna Sohna J, Spence EJ, Stevens K, Sutton N, Szajkowski L, Tregidgo CL, Turcatti G, Vandevondele S, Verhovsky Y, Virk SM, Wakelin S, Walcott GC, Wang JW, Worsley GJ, Yan JY, Yau L, Zuerlein M, Rogers J, Mullikin JC, Hurles ME, McCooke NJ, West JS, Oaks FL, Lundberg PL, Klenerman D, Durbin R, Smith AJ. Accurate whole human genome sequencing using reversible terminator chemistry. Nature , 2008, 456(7218): 53-59. [9] Valouev A, Ichikawa J, Tonthat T, Stuart J, Ranade S, Peckham H, Zeng K, Malek JA, Costa G, McKernan K, Sidow A, Fire A, Johnson SM. A high-resolution, nucleosome position map of C. elegans reveals a lack of universal sequence-dictated positioning. Genome Res , 2008, 18(7): 1051-1063. [10] 杨晓玲, 施苏华, 唐恬. 新一代测序技术的发展及应用前景. 生物技术通报, 2010, (10): 76-81. [11] 1000 Genomes Project Consortium, Abecasis GR, Auton A, Brooks LD, DePristo MA, Durbin RM, Handsaker RE, Kang HM, Marth GT, McVean GA. An integrated map of genetic variation from 1, 092 human genomes. Nature , 2012, 491(7422): 56-65. [12] Haussler D, O'Brien S J, Ryder OA, Barker FK, Clamp M, Crawford AJ, Hanner R, Hanotte O, Johnson WE, McGuire JA, Miller W, Murphy RW, Murphy WJ, Sheldon FH, Sinervo B, Venkatesh B, Wiley EO, Allendorf FW, Amato G, Baker CS, Bauer A, Beja-Pereira A, Bermingham E, Bernardi G, Bonvicino CR, Brenner S, Burke T, Cracraft J, Diekhans M, Edwards S, Ericson PG, Estes J, Fjelsda J, Flesness N, Gamble T, Gaubert P, Graphodatsky AS, Marshall Graves JA, Green ED, Green RE, Hackett S, Hebert P, Helgen KM, Joseph L, Kessing B, Kingsley DM, Lewin HA, Luikart G, Martelli P, Moreira MA, Nguyen N, Ortí G, Pike BL, Rawson DM, Schuster SC, Seuánez HN, Shaffer HB, Springer MS, Stuart JM, Sumner J, Teeling E, Vrijenhoek RC, Ward RD, Warren WC, Wayne R, Williams TM, Wolfe ND, Zhang YP. Genome 10K: a proposal to obtain whole-genome sequence for 10 000 vertebrate species. J Hered , 2009, 100(6): 659-674. [13] Shin SC, Ahn do H, Kim SJ, Lee H, Oh TJ, Lee JE, Park H. Advantages of single-molecule real-time sequencing in high-GC content genomes. PLoS One , 2013, 8(7): e68824. [14] 李明爽, 赵敏. 第三代测序基本原理. 现代生物医学进展, 2012, 12(10): 1980-1982. [15] Levene MJ, Korlach J, Turner SW, Foquet M, Craighead HG, Webb WW. Zero-mode waveguides for single-molecule analysis at high concentrations. Science , 2003, 299(5607): 682-686. [16] Eid J, Fehr A, Gray J, Luong K, Lyle J, Otto G, Peluso P, Rank D, Baybayan P, Bettman B, Bibillo A, Bjornson K, Chaudhuri B, Christians F, Cicero R, Clark S, Dalal R, Dewinter A, Dixon J, Foquet M, Gaertner A, Hardenbol P, Heiner C, Hester K, Holden D, Kearns G, Kong XX, Kuse R, Lacroix Y, Lin S, Lundquist P, Ma CC, Marks P, Maxham M, Murphy D, Park I, Pham T, Phillips M, Roy J, Sebra R, Shen G, Sorenson J, Tomaney A, Travers K, Trulson M, Vieceli J, Wegener J, Wu D, Yang A, Zaccarin D, Zhao P, Zhong F, Korlach J, Turner S. Real-time DNA sequencing from single polymerase molecules. Science , 2009, 323(5910): 133-138. [17] Heiner C, Baybayan P, Wang S, Guo Y, Ashby M, Wilson J, Travers K, Chin J, Underwood J. Greater than 10 kb read lengths routine when sequencing with Pacific Biosciences’ XL release. J Biomol Tech , 2013, 24(S): S43. [18] Mosher JJ, Bowman B, Bernberg EL, Shevchenko O, Kan JJ, Korlach J, Kaplan LA. Improved performance of the PacBio SMRT technology for 16S rDNA sequencing. J Microbiol Methods , 2014, 104: 59-60. [19] Sharon D, Tilgner H, Grubert F, Snyder M. A single-molecule long-read survey of the human transcriptome. Nat Biotechnol , 2013, 31(11): 1009-1014. [20] Treutlein B, Gokce O, Quake SR, Südhof TC. Cartography of neurexin alternative splicing mapped by single-molecule long-read mRNA sequencing. Proc Natl Acad Sci USA , 2014, 111(13): E1291-E1299. [21] Aird D, Ross MG, Chen WS, Danielsson M, Fennell T, Russ C, Jaffe DB, Nusbaum C, Gnirke A. Analyzing and minimizing PCR amplification bias in Illumina sequencing libraries. Genome Biol , 2011, 12(2): R18. [22] Niu BF, Fu LM, Sun SL, Li WZ. Artificial and natural duplicates in pyrosequencing reads of metagenomic data. BMC Bioinform , 2010, 11: 187. [23] Dohm JC, Lottaz C, Borodina T, Himmelbauer H. Substantial biases in ultra-short read data sets from high- throughput DNA sequencing. Nucleic Acids Res , 2008, 36(16): e105. [24] Schadt EE, Turner S, Kasarskis A. A window into third- generation sequencing. Hum Mol Genet , 2010, 19(R2): R227-R240. [25] 刘岩, 吴秉铨. 第三代测序技术: 单分子即时测序. 中华病理学杂志, 2011, 40(10): 718-720. [26] Flusberg BA, Webster DR, Lee JH, Travers KJ, Olivares EC, Clark TA, Korlach J, Turner SW. Direct detection of DNA methylation during single-molecule, real-time sequencing. Nat Methods , 2010, 7(6): 461-465. [27] Kriaucionis S, Heintz N. The nuclear DNA base 5-hydroxymethylcytosine is present in Purkinje neurons and the brain. Science , 2009, 324(5929): 929-930. [28] 张得芳, 马秋月, 尹佟明, 夏涛. 第三代测序技术及其应用. 中国生物工程杂志, 2013, 33(5): 125-131. [29] Uemura S, Aitken CE, Korlach J, Flusberg BA, Turner SW, Puglisi JD. Real-time tRNA transit on single translating ribosomes at codon resolution. Nature , 2010, 464(7291): 1012-1017. [30] Chin CS, Alexander DH, Marks P, Klammer AA, Drake J, Heiner C, Clum A, Copeland A, Huddleston J, Eichler EE, Turner SW, Korlach J. Nonhybrid, finished microbial genome assemblies from long-read SMRT sequencing data. Nat Methods , 2013, 10(6): 563-569. [31] Gnerre S, MacCallum I, Przybylski D, Ribeiro FJ, Burton JN, Walker BJ, Sharpe T, Hall G, Shea TP, Sykes S, Berlin AM, Aird D, Costello M, Daza R, Williams L, Nicol R, Gnirke A, N J Virol usbaum C, Lander ES, Jaffe DB. High-quality draft assemblies of mammalian genomes from massively parallel sequence data. Proc Natl Acad Sci USA , 2011, 108(4): 1513-1518. [32] Bashir A, Klammer AA, Robins WP, Chin CS, Webster D, Paxinos E, Hsu D, Ashby M, Wang S, Peluso P, Sebra R, Sorenson J, Bullard J, Yen J, Valdovino M, Mollova E, Luong K, Lin S, LaMay B, Joshi A, Rowe L, Frace M, Tarr CL, Turnsek M, Davis BM, Kasarskis A, Mekalanos JJ, Waldor MK, Schadt EE. A hybrid approach for the automated finishing of bacterial genomes. Nat Biotechnol , 2012, 30(7): 701-707. [33] Chevreux B. MIRA: an automated genome and EST assembler[Ph. D. Thesis]. Duisburg: Heidelberg, 2005. [34] Koren S, Schatz MC, Walenz BP, Martin J, Howard JT, Ganapathy G, Wang Z, Rasko DA, McCombie WR, Jarvis ED, Phillippy AM. Hybrid error correction and de novo assembly of single-molecule sequencing reads. Nat Biotechnol , 2012, 30(7): 693-700. [35] Chaisson MJ, Tesler G. Mapping single molecule sequencing reads using basic local alignment with successive refinement (BLASR): application and theory. BMC Bioinform , 2012, 13(1): 238. [36] Au KF, Underwood JG, Lee L, Wong WH. Improving PacBio long read accuracy by short read alignment. PLoS One , 2012, 7(10): e46679. [37] English AC, Richards S, Han Y, Wang M, Vee V, Qu JX, Qin X, Muzny DM, Reid JG, Worley KC, Gibbs RA. Mind the gap: upgrading genomes with Pacific Biosciences RS long-read sequencing technology. PLoS One , 2012, 7(11): e47768. [38] Ono Y, Asai K, Hamada M. PBSIM: PacBio reads simulator—toward accurate genome assembly. Bioinformatics , 2013, 29(1): 119-121. [39] Coupland P, Chandra T, Quail M, Reik W, Swerdlow H. Direct sequencing of small genomes on the Pacific Biosciences RS without library preparation. Biotechniques , 2012, 53(6): 365-372. [40] Youssef NH, Couger MB, Struchtemeyer CG, Liggenstoffer AS, Prade RA, Najar FZ, Atiyeh HK, Wilkins MR, Elshahed MS. The genome of the anaerobic fungus Orpinomyces sp. strain C1A reveals the unique evolutionary history of a remarkable plant biomass degrader. Appl Environ Microbiol , 2013, 79(15): 4620-4634. [41] Schmuki MM, Erne D, Loessner MJ, Klumpp J. Bacteriophage P70: Unique morphology and unrelatedness to other Listeria bacteriophages. J Virol , 2012, 86(23): 13099-13102. [42] Carneiro MO, Russ C, Ross MG, Gabriel SB, Nusbaum C, DePristo MA. Pacific biosciences sequencing technology for genotyping and variation discovery in human data. BMC Genom , 2012, 13(1): 375. [43] Loomis EW, Eid JS, Peluso P, Yin J, Hickey L, Rank D, McCalmon S, Hagerman RJ, Tassone F, Hagerman PJ. Sequencing the unsequenceable: Expanded CGG-repeat alleles of the fragile X gene. Genome Res , 2013, 23(1): 121-128. [44] Song CX, Clark TA, Lu XY, Kislyuk A, Dai Q, Turner SW, He C, Korlach J. Sensitive and specific single-molecule sequencing of 5-hydroxymethylcytosine. Nat Methods , 2012, 9(1): 75-77. [45] Fang G, Munera D, Friedman DI, Mandlik A, Chao MC, Banerjee O, Feng ZX, Losic B, Mahajan MC, Jabado OJ, Deikus G, Clark TA, Luong K, Murray IA, Davis BM, Keren-Paz A, Chess A, Roberts RJ, Korlach J, Turner SW, Kumar V, Waldor MK, Schadt EE. Genome-wide mapping of methylated adenine residues in pathogenic Escherichia coli using single-molecule real-time sequencing. Nat Biotechnol , 2012, 30(12): 1232-1239. [46] Schadt EE, Banerjee O, Fang G, Feng ZX, Wong WH, Zhang XG, Kislyuk A, Clark TA, Luong K, Keren-Paz A, Chess A, Kumar V, Chen-Plotkin A, Sondheimer N, Korlach J, Kasarskis A. Modeling kinetic rate variation in third generation DNA sequencing data to detect putative modifications to DNA bases. Genome Res , 2013, 23(1): 129-141. [47] Lluch-Senar M, Luong K, Lloréns-Rico V, Delgado J, Fang G, Spittle K, Clark TA, Schadt E, Turner SW, Korlach J, Serrano L. Comprehensive methylome characterization of Mycoplasma genitalium and Mycoplasma pneumoniae at single-base resolution. PLoS Genet , 2013, 9(1): e1003191. [48] Vilfan ID, Tsai YC, Clark TA, Wegener J, Dai Q, Yi CQ, Pan T, Turner SW, Korlach J. Analysis of RNA base modification and structural rearrangement by single-molecule real-time detection of reverse transcription. J Nanobiotechn , 2013, 11(1): 8. [49] Ocwieja KE, Sherrill-Mix S, Mukherjee R, Custers-Allen R, David P, Brown M, Wang S, Link DR, Olson J, Travers K, Schadt E, Bushman FD. Dynamic regulation of HIV-1 mRNA populations analyzed by single-molecule enrichment and long-read sequencing. Nucleic Acids Res , 2012, 40(20): 10345-10355. [50] Li QS, Li Y, Song JY, Xu HB, Xu J, Zhu YJ, Li XW, Gao HH, Dong LL, Qian J, Sun C, Chen SL. High-accuracy de novo assembly and SNP detection of chloroplast genomes using a SMRT circular consensus sequencing strategy. New Phytol , 2014, 204(4): 1041-1049. [51] Ferrarini M, Moretto M, Ward JA, Šurbanovski N, Stevanović V, Giongo L, Viola R, Cavalieri D, Velasco R, Cestaro A, Sargent DJ. An evaluation of the PacBio RS platform for sequencing and de novo assembly of a chloroplast genome. BMC Genom , 2013, 14(1): 670. [52] Murray IA, Clark TA, Morgan RD, Boitano M, Anton BP, Luong K, Fomenkov A, Turner SW, Korlach J, Roberts RJ. The methylomes of six bacteria. Nucleic Acids Res , 2012, 40(22): 11450-11462. [53] 王兴春, 杨致荣, 王敏, 李玮, 李生才. 高通量测序技术及其应用. 中国生物工程杂志, 2012, 32(1): 109-114. [54] Harris TD, Buzby PR, Babcock H, Beer E, Bowers J, Braslavsky I, Causey M, Colonell J, DiMeo J, Efcavitch JW, Giladi E, Gill J, Healy J, Jarosz M, Lapen D, Moulton K, Quake SR, Steinmann K, Thayer E, Tyurina A, Ward R, Weiss H, Xie Z. Single-molecule DNA sequencing of a viral genome. Science , 2008, 320(5872): 106-109. |