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Volumn 855, Issue , 2012, Pages 155-174

Next-generation sequencing technologies and fragment assembly algorithms

Author keywords

de Bruijn graph; Fragment assembly algorithms; Genome sequencing; Next generation sequencing; Overlap graph

Indexed keywords

ALGORITHM; ANIMAL; ARTICLE; BIOLOGY; DNA SEQUENCE; HIGH THROUGHPUT SEQUENCING; HUMAN; METHODOLOGY;

EID: 84860015746     PISSN: 10643745     EISSN: None     Source Type: Book Series    
DOI: 10.1007/978-1-61779-582-4_5     Document Type: Article
Times cited : (18)

References (67)
  • 2
    • 42249087308 scopus 로고    scopus 로고
    • The complete genome of an individual by massively parallel DNA sequencing
    • Wheeler, D., et al. (2008) The complete genome of an individual by massively parallel DNA sequencing. Nature, 452, 872-876.
    • (2008) Nature , vol.452 , pp. 872-876
    • Wheeler, D.1
  • 3
    • 55549089660 scopus 로고    scopus 로고
    • Accurate whole human genome sequencing using reversible terminator chemistry
    • Bentley, D., et al. (2008) Accurate whole human genome sequencing using reversible terminator chemistry. Nature, 456, 53-59.
    • (2008) Nature , vol.456 , pp. 53-59
    • Bentley, D.1
  • 4
    • 55549097849 scopus 로고    scopus 로고
    • The diploid genome sequence of an Asian individual
    • Wang, J., et al. (2008) The diploid genome sequence of an Asian individual. Nature, 456, 60-65.
    • (2008) Nature , vol.456 , pp. 60-65
    • Wang, J.1
  • 5
    • 69249232047 scopus 로고    scopus 로고
    • A highly annotated whole-genome sequence of a Korean individual
    • Kim, J., et al. (2009) A highly annotated whole-genome sequence of a Korean individual. Nature, 460, 1011-1015.
    • (2009) Nature , vol.460 , pp. 1011-1015
    • Kim, J.1
  • 6
    • 34547633677 scopus 로고    scopus 로고
    • Genome-wide profiles of STAT1 DNA association using chromatin immunoprecipitation and massively parallel sequencing
    • Robertson, G., et al. (2007) Genome-wide profiles of STAT1 DNA association using chromatin immunoprecipitation and massively parallel sequencing. Nature Methods, 4, 651-657.
    • (2007) Nature Methods , vol.4 , pp. 651-657
    • Robertson, G.1
  • 7
    • 57749195712 scopus 로고    scopus 로고
    • RNA-Seq: A revolutionary tool for transcriptomics
    • Wang, Z., Gerstein, M., and Snyder,M. (2009) RNA-Seq: a revolutionary tool for transcriptomics. Nature Reviews Genetics, 10, 57-63.
    • (2009) Nature Reviews Genetics , vol.10 , pp. 57-63
    • Wang, Z.1    Gerstein, M.2    Snyder, M.3
  • 8
    • 70450217879 scopus 로고    scopus 로고
    • Human DNA methylomes at base resolution show widespread epigenomic differences
    • Lister, R., et al. (2009) Human DNA methylomes at base resolution show widespread epigenomic differences. Nature, 462, 315-322.
    • (2009) Nature , vol.462 , pp. 315-322
    • Lister, R.1
  • 9
    • 70249111091 scopus 로고    scopus 로고
    • Targeted capture and assively parallel sequencing of 12 human exomes
    • Ng, S., et al. (2009) Targeted capture and assively parallel sequencing of 12 human exomes. Nature, 461, 272-276.
    • (2009) Nature , vol.461 , pp. 272-276
    • Ng, S.1
  • 10
    • 0032540905 scopus 로고    scopus 로고
    • A sequencing method based on real-time pyrophosphate
    • Washington
    • Ronaghi, M., Uhlen, M., and Nyren, P. (1998) A sequencing method based on real-time pyrophosphate. Science(Washington), 281, 363-365.
    • (1998) Science , vol.281 , pp. 363-365
    • Ronaghi, M.1    Uhlen, M.2    Nyren, P.3
  • 11
    • 0034130561 scopus 로고    scopus 로고
    • Gene expression analysis by massively parallel signature sequencing MPSS on microbead arrays
    • Brenner, S., et al. (2000) Gene expression analysis by massively parallel signature sequencing (MPSS) on microbead arrays. Nature biotechnology, 18, 630-634.
    • (2000) Nature Biotechnology , vol.18 , pp. 630-634
    • Brenner, S.1
  • 12
    • 34948842866 scopus 로고    scopus 로고
    • Accuracy and quality of massively parallel DNA pyrosequencing
    • Huse, S., Huber, J., Morrison, H., Sogin, M., and Welch, D. (2007) Accuracy and quality of massively parallel DNA pyrosequencing. Genome Biology, 8, R143.
    • (2007) Genome Biology , vol.8
    • Huse, S.1    Huber, J.2    Morrison, H.3    Sogin, M.4    Welch, D.5
  • 13
    • 77952886150 scopus 로고    scopus 로고
    • Assembly algorithms for next-generation sequencing data
    • Miller, J., Koren, S., and Sutton, G. (2010) Assembly algorithms for next-generation sequencing data. Genomics, 95, 315-327.
    • (2010) Genomics , vol.95 , pp. 315-327
    • Miller, J.1    Koren, S.2    Sutton, G.3
  • 14
    • 55549097836 scopus 로고    scopus 로고
    • Mapping short DNA sequencing reads and calling variants using mapping quality scores
    • Li, H., Ruan, J., and Durbin, R. (2008) Mapping short DNA sequencing reads and calling variants using mapping quality scores. Genome Research, 18, 1851.
    • (2008) Genome Research , vol.18 , pp. 1851
    • Li, H.1    Ruan, J.2    Durbin, R.3
  • 15
    • 62349130698 scopus 로고    scopus 로고
    • Ultra-fast and memoryefficient alignment of short DNA sequences to the human genome
    • Langmead, B., Trapnell, C., Pop, M., and Salzberg, S. (2009) Ultra-fast and memoryefficient alignment of short DNA sequences to the human genome. Genome Biol, 10, R25.
    • (2009) Genome Biol. , vol.10
    • Langmead, B.1    Trapnell, C.2    Pop, M.3    Salzberg, S.4
  • 16
    • 77949587649 scopus 로고    scopus 로고
    • Fast and accurate long-read alignment with burrows-wheeler transform
    • Li, H. and Durbin, R. (2010) Fast and accurate long-read alignment with Burrows-Wheeler transform. Bioinformatics, 26, 589.
    • (2010) Bioinformatics , vol.26 , pp. 589
    • Li, H.1    Durbin, R.2
  • 17
    • 70349556543 scopus 로고    scopus 로고
    • Personalized copy number and segmental duplication maps using next-generation sequencing
    • Alkan, C., et al. (2009) Personalized copy number and segmental duplication maps using next-generation sequencing. Nature Genetics, 41, 1061-1067.
    • (2009) Nature Genetics , vol.41 , pp. 1061-1067
    • Alkan, C.1
  • 18
    • 70450177746 scopus 로고    scopus 로고
    • Bfast: An alignment tool for large scale genome resequencing
    • Homer, N., Merriman, B., and Nelson, S. (2009) BFAST: an alignment tool for large scale genome resequencing. PLoSOne, 4, e7767.
    • (2009) PLoS One , vol.4
    • Homer, N.1    Merriman, B.2    Nelson, S.3
  • 19
    • 40049104732 scopus 로고    scopus 로고
    • Soap: Short oligonucleotide alignment program
    • Li, R., Li, Y., Kristiansen, K., and Wang, J. (2008) SOAP: short oligonucleotide alignment program. Bioinformatics, 24, 713.
    • (2008) Bioinformatics , vol.24 , pp. 713
    • Li, R.1    Li, Y.2    Kristiansen, K.3    Wang, J.4
  • 20
    • 34547295064 scopus 로고    scopus 로고
    • Jigsaw puzzles edge matching and polyomino packing: Connections and complexity
    • Demaine, E. and Demaine, M. (2007) Jigsaw puzzles, edge matching, and polyomino packing: Connections and complexity. Graphs and Combinatorics, 23, 195-208.
    • (2007) Graphs and Combinatorics , vol.23 , pp. 195-208
    • Demaine, E.1    Demaine, M.2
  • 21
    • 0018426987 scopus 로고
    • A strategy of DNA sequencing employing computer programs
    • Staden, R. (1979) A strategy of DNA sequencing employing computer programs. Nucleic Acids Research, 6, 2601.
    • (1979) Nucleic Acids Research , vol.6 , pp. 2601
    • Staden, R.1
  • 22
    • 0023988195 scopus 로고
    • Genomic mapping by finger-printing random clones: A mathematical analysis
    • Lander, E. andWaterman, M. (1988) Genomic mapping by finger-printing random clones: a mathematical analysis. Genomics, 2, 231-239.
    • (1988) Genomics , vol.2 , pp. 231-239
    • Lander, E.1    Waterman, M.2
  • 23
    • 0029312158 scopus 로고
    • Toward simplifying and accurately formulating fragment assembly
    • Myers, E. (1995) Toward simplifying and accurately formulating fragment assembly. Journal of Computational Biology, 2, 275-290.
    • (1995) Journal of Computational Biology , vol.2 , pp. 275-290
    • Myers, E.1
  • 25
    • 0001899550 scopus 로고
    • TIGR Assembler: A new tool for assembling large shotgun sequencing projects
    • Sutton, G., White, O., Adams, M., and Kerlavage, A. (1995) TIGR Assembler: A new tool for assembling large shotgun sequencing projects. Genome Science and Technology, 1, 9-19.
    • (1995) Genome Science and Technology , vol.1 , pp. 9-19
    • Sutton, G.1    White, O.2    Adams, M.3    Kerlavage, A.4
  • 26
    • 0032849859 scopus 로고    scopus 로고
    • CAP3: A DNA sequence assembly program
    • Huang, X. and Madan, A. (1999) CAP3: A DNA sequence assembly program. Genome research, 9, 868.
    • (1999) Genome research , vol.9 , pp. 868
    • Huang, X.1    Madan, A.2
  • 27
    • 0034708758 scopus 로고    scopus 로고
    • A whole-genome assembly of drosophila
    • Myers, E., et al. (2000) A whole-genome assembly of Drosophila. Science, 287, 2196.
    • (2000) Science , vol.287 , pp. 2196
    • Myers, E.1
  • 30
    • 0346505466 scopus 로고    scopus 로고
    • Hierarchical scaffolding with bambus
    • Pop, M., Kosack, D., and Salzberg, S. (2004) Hierarchical scaffolding with Bambus. Genome Research, 14, 149.
    • (2004) Genome Research , vol.14 , pp. 149
    • Pop, M.1    Kosack, D.2    Salzberg, S.3
  • 31
    • 77957758142 scopus 로고    scopus 로고
    • Reptile: Representative tiling for short read error correction
    • Yang, X., Dorman, K., and Aluru, S. (2010) Reptile: Representative Tiling for Short Read Error Correction. Bioinformatics, 26, 2526
    • (2010) Bioinformatics , vol.26 , pp. 2526
    • Yang, X.1    Dorman, K.2    Aluru, S.3
  • 32
    • 78649358717 scopus 로고    scopus 로고
    • Quake: Quality-aware detection and correction of sequencing errors
    • Kelley, D., Schatz, M., and Salzberg, S. (2010) Quake: quality-aware detection and correction of sequencing errors. Genome Biology, 11, R116.
    • (2010) Genome Biology , vol.11
    • Kelley, D.1    Schatz, M.2    Salzberg, S.3
  • 33
    • 45549109750 scopus 로고    scopus 로고
    • Genome assembly forensics: Finding the elusive mis-assembly
    • Phillippy, A., Schatz, M., and Pop, M. (2008) Genome assembly forensics: finding the elusive mis-assembly. Genome Biology, 9, R55.
    • (2008) Genome Biology , vol.9
    • Phillippy, A.1    Schatz, M.2    Pop, M.3
  • 34
    • 40749116115 scopus 로고    scopus 로고
    • A machinelearningapproach to combined evidence validation of genome assemblies
    • Choi, J., Kim, S., Tang, H., Andrews, J., Gilbert, D., and Colbourne, J. (2008) A machinelearningapproach to combined evidence validation of genome assemblies. Bioinformatics, 24, 744.
    • (2008) Bioinformatics , vol.24 , pp. 744
    • Choi, J.1    Kim, S.2    Tang, H.3    Andrews, J.4    Gilbert, D.5    Colbourne, J.6
  • 35
    • 0031955116 scopus 로고    scopus 로고
    • Consed: A graphical tool for sequence finishing
    • Gordon, D., Abajian, C., and Green, P. (1998) Consed: a graphical tool for sequence finishing. Genome Research, 8, 195.
    • (1998) Genome Research , vol.8 , pp. 195
    • Gordon, D.1    Abajian, C.2    Green, P.3
  • 37
    • 34250210806 scopus 로고    scopus 로고
    • Hawkeye: An interactive visual analytics tool for genome assemblies
    • Schatz, M., Phillippy, A., Shneiderman, B., and Salzberg, S. (2007) Hawkeye: an interactive visual analytics tool for genome assemblies. Genome Biology, 8, R34.
    • (2007) Genome Biology , vol.8
    • Schatz, M.1    Phillippy, A.2    Shneiderman, B.3    Salzberg, S.4
  • 38
    • 41249098849 scopus 로고    scopus 로고
    • A high quality draft consensus sequence of the genome of a heterozygous grapevine variety
    • Velasco, R., et al. (2007) A high quality draft consensus sequence of the genome of a heterozygous grapevine variety. PLoS One, 2, 1326.
    • (2007) PLoS One , vol.2 , pp. 1326
    • Velasco, R.1
  • 39
    • 33746605947 scopus 로고    scopus 로고
    • A sanger pyrosequencing hybrid approach for the generation of high-quality draft assemblies of marine microbial genomes
    • Goldberg, S., et al. (2006) A Sanger/pyrosequencing hybrid approach for the generation of high-quality draft assemblies of marine microbial genomes. Proceedings of the National Academy of Sciences, 103, 11240.
    • (2006) Proceedings of the National Academy of Sciences , vol.103 , pp. 11240
    • Goldberg, S.1
  • 40
    • 70649085835 scopus 로고    scopus 로고
    • The genome of the cucumber cucumis sativus L
    • Huang, S., et al. (2009) The genome of the cucumber, Cucumis sativus L. Nature Genetics, 41, 1275-1281.
    • (2009) Nature Genetics , vol.41 , pp. 1275-1281
    • Huang, S.1
  • 41
    • 59949090259 scopus 로고    scopus 로고
    • De novo assembly using low-coverage short read sequence data from the rice pathogen pseudomonas syringae pv oryzae
    • Reinhardt, J., Baltrus, D., Nishimura, M., Jeck, W., Jones, C., and Dangl, J. (2009) De novo assembly using low-coverage short read sequence data from the rice pathogen Pseudomonas syringae pv. oryzae. Genome Research, 19, 294.
    • (2009) Genome Research , vol.19 , pp. 294
    • Reinhardt, J.1    Baltrus, D.2    Nishimura, M.3    Jeck, W.4    Jones, C.5    Dangl, J.6
  • 42
    • 46249087524 scopus 로고    scopus 로고
    • A robust framework for detecting structural variations in a genome
    • Lee, S., Cheran, E., and Brudno, M. (2008) A robust framework for detecting structural variations in a genome. Bioinformatics, 24, i59.
    • (2008) Bioinformatics , vol.24
    • Lee, S.1    Cheran, E.2    Brudno, M.3
  • 43
    • 67650064593 scopus 로고    scopus 로고
    • Combinatorial algorithms for structural variation detection in highthroughput sequenced genomes
    • Hormozdiari, F., Alkan, C., Eichler, E., and Sahinalp, S. (2009) Combinatorial algorithms for structural variation detection in highthroughput sequenced genomes. Genome Research, 19, 1270.
    • (2009) Genome Research , vol.19 , pp. 1270
    • Hormozdiari, F.1    Alkan, C.2    Eichler, E.3    Sahinalp, S.4
  • 44
    • 67649580757 scopus 로고    scopus 로고
    • MoDIL: Detecting small indels from clone-end sequencing with mixtures of distributions
    • Lee, S.,Hormozdiari, F., Alkan,C., and Brudno, M. (2009) MoDIL: detecting small indels from clone-end sequencing with mixtures of distributions. Nature Methods, 6, 473-474.
    • (2009) Nature Methods , vol.6 , pp. 473-474
    • Lee, S.1    Hormozdiari, F.2    Alkan, C.3    Brudno, M.4
  • 45
    • 69549116107 scopus 로고    scopus 로고
    • Break dancer: An algorithm for high-resolution mapping of genomic structural variation
    • Chen, K., et al. (2009) BreakDancer: an algorithm for high-resolution mapping of genomic structural variation. Nature Methods, 6, 677-681.
    • (2009) Nature Methods , vol.6 , pp. 677-681
    • Chen, K.1
  • 46
    • 70350694443 scopus 로고    scopus 로고
    • Pindel: A pattern growth approach to detect break points of large deletions and medium sized insertions from paired-end short reads
    • Ye, K., Schulz, M., Long, Q., Apweiler, R., and Ning, Z. (2009) Pindel: a pattern growth approach to detect break points of large deletions and medium sized insertions from paired-end short reads. Bioinformatics, 25, 2865.
    • (2009) Bioinformatics , vol.25 , pp. 2865
    • Ye, K.1    Schulz, M.2    Long, Q.3    Apweiler, R.4    Ning, Z.5
  • 48
    • 52949083195 scopus 로고    scopus 로고
    • Gene-boosted assembly of a novel bacterial genome from very short reads
    • Salzberg, S., Sommer, D., Puiu, D., and Lee, V. (2008) Gene-boosted assembly of a novel bacterial genome from very short reads. PLoS Comput Biol, 4, e1000186.
    • (2008) PLoS Comput. Biol. , vol.4
    • Salzberg, S.1    Sommer, D.2    Puiu, D.3    Lee, V.4
  • 49
    • 49549099085 scopus 로고    scopus 로고
    • HapCUT: An efficient and accurate algorithm for the haplotype assembly problem
    • Bansal, V. and Bafna, V. (2008) HapCUT: an efficient and accurate algorithm for the haplotype assembly problem. Bioinformatics, 24, i153.
    • (2008) Bioinformatics , vol.24
    • Bansal, V.1    Bafna, V.2
  • 50
    • 35648976118 scopus 로고    scopus 로고
    • The diploid genome sequence of an individual human
    • Levy, S., et al. (2007) The diploid genome sequence of an individual human. PLoS Biol, 5, e254.
    • (2007) PLoS Biol. , vol.5
    • Levy, S.1
  • 53
    • 65449136284 scopus 로고    scopus 로고
    • Tophat: Discovering splice junctions with RNA-Seq
    • Trapnell, C., Pachter, L., and Salzberg, S. (2009) TopHat: discovering splice junctions with RNA-Seq. Bioinformatics, 25, 1105.
    • (2009) Bioinformatics , vol.25 , pp. 1105
    • Trapnell, C.1    Pachter, L.2    Salzberg, S.3
  • 54
    • 78649345104 scopus 로고    scopus 로고
    • Map splice: Accurate mapping of RNA-seq reads for splice junction discovery
    • Wang, K., et al. (2010) MapSplice: Accurate mapping of RNA-seq reads for splice junction discovery. Nucleic Acids Research, 38, e178.
    • (2010) Nucleic Acids Research , vol.38
    • Wang, K.1
  • 55
    • 77952123055 scopus 로고    scopus 로고
    • Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoformswitching during cell differentiation
    • Trapnell, C., Williams, B., Pertea, G., Mortazavi, A., Kwan, G., Van Baren, M., Salzberg, S., Wold, B., and Pachter, L. (2010) Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoformswitching during cell differentiation. NatureBiotechnology, 28, 511-515.
    • (2010) Nature Biotechnology , vol.28 , pp. 511-515
    • Trapnell, C.1    Williams, B.2    Pertea, G.3    Mortazavi, A.4    Kwan, G.5    Van Baren, M.6    Salzberg, S.7    Wold, B.8    Pachter, L.9
  • 56
    • 33847307402 scopus 로고    scopus 로고
    • Assembling millions of short DNA sequences using SSAKE
    • Warren, R., Sutton, G., Jones, S., and Holt, R. (2007) Assembling millions of short DNA sequences using SSAKE. Bioinformatics, 23,500.
    • (2007) Bioinformatics , vol.23 , pp. 500
    • Warren, R.1    Sutton, G.2    Jones, S.3    Holt, R.4
  • 61
    • 3042615882 scopus 로고    scopus 로고
    • Using the miraEST assembler for reliableand automated mRNA transcript assemblyand SNP detection in sequenced ESTs
    • Chevreux, B., Pfisterer, T., Drescher, B., Driesel,A., Muller, W., Wetter, T., and Suhai, S.(2004) Using the miraEST assembler for reliableand automated mRNA transcript assemblyand SNP detection in sequenced ESTs. GenomeResearch, 14, 1147.
    • (2004) Genome Research , vol.14 , pp. 1147
    • Chevreux, B.1    Pfisterer, T.2    Drescher, B.3    Driesel, A.4    Muller, W.5    Wetter, T.6    Suhai, S.7
  • 63
    • 39049156065 scopus 로고    scopus 로고
    • Short read fragment assembly of bacterial genomes
    • Chaisson, M. and Pevzner, P. (2008) Short read fragment assembly of bacterial genomes.Genome Research, 18, 324.
    • (2008) Genome Research , vol.18 , pp. 324
    • Chaisson, M.1    Pevzner, P.2
  • 64
    • 43149115851 scopus 로고    scopus 로고
    • Velvet: Algorithms for de novo short read assembly usingde bruijn graphs
    • Zerbino, D. and Birney, E. (2008) Velvet: algorithms for de novo short read assembly usingde Bruijn graphs. Genome Research, 18, 821.
    • (2008) Genome Research , vol.18 , pp. 821
    • Zerbino, D.1    Birney, E.2
  • 67
    • 75649124547 scopus 로고    scopus 로고
    • De novo assembly ofhuman genomes with massively parallel short read sequencing
    • Li, R., et al. (2010) De novo assembly ofhuman genomes with massively parallel short read sequencing. Genome Research, 20, 265
    • (2010) Genome Research , vol.20 , pp. 265
    • Li, R.1


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