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Volumn 13, Issue 3, 2012, Pages 269-280

Comparative analysis of algorithms for whole-genome assembly of pyrosequencing data

Author keywords

454 pyrosequencing; Assembly algorithm assessment; Bacterial genome; Coverage

Indexed keywords

ALGORITHM; ANIMAL; ARTICLE; COMPARATIVE STUDY; DNA SEQUENCE; GENOME; GENOMICS; HUMAN; METHODOLOGY;

EID: 82255165034     PISSN: 14675463     EISSN: 14774054     Source Type: Journal    
DOI: 10.1093/bib/bbr063     Document Type: Article
Times cited : (23)

References (39)
  • 1
    • 53649106195 scopus 로고    scopus 로고
    • Next-generation DNA sequencing
    • Shendure J, Ji H. Next-generation DNA sequencing. Nat Biotechnol 2008;26:1135-45.
    • (2008) Nat Biotechnol , vol.26 , pp. 1135-1145
    • Shendure, J.1    Ji, H.2
  • 2
    • 39649117755 scopus 로고    scopus 로고
    • The impact of next-generation sequencing technology on genetics
    • Mardis ER. The impact of next-generation sequencing technology on genetics. TrendsGenet 2008;24:133-41.
    • (2008) TrendsGenet , vol.24 , pp. 133-141
    • Mardis, E.R.1
  • 3
    • 0035925596 scopus 로고    scopus 로고
    • Reverse vaccinology, a genome-based approach to vaccine development
    • Rappuoli R. Reverse vaccinology, a genome-based approach to vaccine development. Vaccine 2001;19:2688-91.
    • (2001) Vaccine , vol.19 , pp. 2688-2691
    • Rappuoli, R.1
  • 4
    • 72849144434 scopus 로고    scopus 로고
    • Sequencing technologies-the next generation
    • Metzker ML. Sequencing technologies-the next generation. Nat Rev Genet 2009;11:31-46.
    • (2009) Nat Rev Genet , vol.11 , pp. 31-46
    • Metzker, M.L.1
  • 5
    • 77952553604 scopus 로고    scopus 로고
    • Next-generation sequencing in aging research: emerging applications, problems, pitfalls and possible solutions
    • de Magalha{ogonek}es JP, Finch CE, Janssens G. Next-generation sequencing in aging research: emerging applications, problems, pitfalls and possible solutions. Ageing Res Rev 2010;9: 315-23.
    • (2010) Ageing Res Rev , vol.9 , pp. 315-323
    • de Magalhaes, J.P.1    Finch, C.E.2    Janssens, G.3
  • 6
    • 79958103038 scopus 로고    scopus 로고
    • The sequence is dead: long live the genome
    • Sheridan C. The sequence is dead: long live the genome. Nat Biotechnol 2011;29:463-6.
    • (2011) Nat Biotechnol , vol.29 , pp. 463-466
    • Sheridan, C.1
  • 7
    • 78650909427 scopus 로고    scopus 로고
    • Limitations of next-generation genome sequence assembly
    • Alkan C, Sajjadian S, Eichler EE. Limitations of next-generation genome sequence assembly. Nat Methods 2010;8:61-5.
    • (2010) Nat Methods , vol.8 , pp. 61-65
    • Alkan, C.1    Sajjadian, S.2    Eichler, E.E.3
  • 8
    • 79955724657 scopus 로고    scopus 로고
    • Comparing De Novo genome assembly: the long and short of it
    • Narzisi G, Mishra B. Comparing De Novo genome assembly: the long and short of it. PLoS ONE 2011;6: e19175.
    • (2011) PLoS ONE , vol.6
    • Narzisi, G.1    Mishra, B.2
  • 9
    • 0030298490 scopus 로고    scopus 로고
    • Real-time DNA sequencing using detection of pyrophosphate release
    • Ronaghi M, Karamohamed S, Pettersson B, et al. Real-time DNA sequencing using detection of pyrophosphate release. Analytical Biochemistry 1996;242:84-9.
    • (1996) Analytical Biochemistry , vol.242 , pp. 84-89
    • Ronaghi, M.1    Karamohamed, S.2    Pettersson, B.3
  • 10
    • 24044455869 scopus 로고    scopus 로고
    • Genome sequencing in microfabricated high-density picolitre reactors
    • Margulies M, Egholm M, Altman WE, et al. Genome sequencing in microfabricated high-density picolitre reactors. Nature 2005;437:376-80.
    • (2005) Nature , vol.437 , pp. 376-380
    • Margulies, M.1    Egholm, M.2    Altman, W.E.3
  • 11
    • 0032540905 scopus 로고    scopus 로고
    • A sequencing method based on real-time pyrophosphate
    • Ronaghi M, Uhlen M, Nyren P. A sequencing method based on real-time pyrophosphate. Science 1998;281: 363-365.
    • (1998) Science , vol.281 , pp. 363-365
    • Ronaghi, M.1    Uhlen, M.2    Nyren, P.3
  • 12
    • 79951665103 scopus 로고    scopus 로고
    • Genome sequence of leuconostoc inhae KCTC 3774 isolated from Kimchi
    • Kim DS, Choi SH, Kim DW, et al. Genome sequence of leuconostoc inhae KCTC 3774, isolated from Kimchi. J Bacteriol 2011;193:1278.
    • (2011) J Bacteriol , vol.193 , pp. 1278
    • Kim, D.S.1    Choi, S.H.2    Kim, D.W.3
  • 13
    • 78650877518 scopus 로고    scopus 로고
    • Complete genome sequence of Japanese Erwinia strain Ejp617, a bacterial shoot blight pathogen of pear
    • Park DH, Thapa SP, Choi BS, et al. Complete genome sequence of Japanese Erwinia strain Ejp617, a bacterial shoot blight pathogen of pear. J Bacteriol 2011; 193:586.
    • (2011) J Bacteriol , vol.193 , pp. 586
    • Park, D.H.1    Thapa, S.P.2    Choi, B.S.3
  • 14
    • 78650164407 scopus 로고    scopus 로고
    • Complete genome sequence of Bifidobacterium bifidum S17
    • Zhurina D, Zomer A, Gleinser M, et al. Complete genome sequence of Bifidobacterium bifidum S17. J Bacteriol 2011;193: 301.
    • (2011) J Bacteriol , vol.193 , pp. 301
    • Zhurina, D.1    Zomer, A.2    Gleinser, M.3
  • 15
    • 77957339244 scopus 로고    scopus 로고
    • Draft genome sequences of two Neisseria meningitidis serogroup C clinical isolates
    • Lavezzo E, Toppo S, Barzon L, et al. Draft genome sequences of two Neisseria meningitidis serogroup C clinical isolates. J Bacteriol 2010;192:5270-1.
    • (2010) J Bacteriol , vol.192 , pp. 5270-5271
    • Lavezzo, E.1    Toppo, S.2    Barzon, L.3
  • 16
    • 77956556252 scopus 로고    scopus 로고
    • Complete genome sequence of Lactobacillus fermentum CECT 5716 a probiotic strain isolated from human milk
    • Jimenez E, Langa S, Martin V, et al. Complete genome sequence of Lactobacillus fermentum CECT 5716, a probiotic strain isolated from human milk. J Bacteriol 2010; 192:4800.
    • (2010) J Bacteriol , vol.192 , pp. 4800
    • Jimenez, E.1    Langa, S.2    Martin, V.3
  • 17
    • 77956505983 scopus 로고    scopus 로고
    • Complete genome sequence of the diesel-degrading Acinetobacter sp. strain DR1
    • Jung J, Baek JH, Park W. Complete genome sequence of the diesel-degrading Acinetobacter sp. strain DR1. J Bacteriol 2010;192:4794-5.
    • (2010) J Bacteriol , vol.192 , pp. 4794-4795
    • Jung, J.1    Baek, J.H.2    Park, W.3
  • 18
    • 57249105124 scopus 로고    scopus 로고
    • Aggressive assembly of pyrosequencing reads with mates
    • Miller JR, Delcher AL, Koren S, et al. Aggressive assembly of pyrosequencing reads with mates. Bioinformatics 2008;24: 2818-24.
    • (2008) Bioinformatics , vol.24 , pp. 2818-2824
    • Miller, J.R.1    Delcher, A.L.2    Koren, S.3
  • 20
    • 0141853948 scopus 로고    scopus 로고
    • PCAP: a whole-genome assembly program
    • Huang X, Wang J, Aluru S, et al. PCAP: a whole-genome assembly program. Genome Res 2003;13:2164-70.
    • (2003) Genome Res , vol.13 , pp. 2164-2170
    • Huang, X.1    Wang, J.2    Aluru, S.3
  • 21
    • 31544479520 scopus 로고    scopus 로고
    • Application of a superword array in genome assembly
    • Huang X, Yang SP, Chinwalla AT, et al. Application of a superword array in genome assembly. Nucleic Acids Res 2006;34:201-5.
    • (2006) Nucleic Acids Res , vol.34 , pp. 201-205
    • Huang, X.1    Yang, S.P.2    Chinwalla, A.T.3
  • 23
    • 43149115851 scopus 로고    scopus 로고
    • Velvet: algorithms for de novo short read assembly using de Bruijn graphs
    • Zerbino DR, Birney E. Velvet: algorithms for de novo short read assembly using de Bruijn graphs. Genome Res 2008;18:821-9.
    • (2008) Genome Res , vol.18 , pp. 821-829
    • Zerbino, D.R.1    Birney, E.2
  • 24
    • 77955076707 scopus 로고    scopus 로고
    • Assembling genomes using short-read sequencing technology
    • Jackman SD, Birol I. Assembling genomes using short-read sequencing technology. Genome Biol 2010;11:202.
    • (2010) Genome Biol , vol.11 , pp. 202
    • Jackman, S.D.1    Birol, I.2
  • 25
    • 77957926979 scopus 로고    scopus 로고
    • Comparing de novo assemblers for 454 transcriptome data
    • Kumar S, Blaxter ML. Comparing de novo assemblers for 454 transcriptome data. BMCGenomics 2010;11:571.
    • (2010) BMCGenomics , vol.11 , pp. 571
    • Kumar, S.1    Blaxter, M.L.2
  • 26
    • 79952655567 scopus 로고    scopus 로고
    • A practical comparison of de novo genome assembly software tools for nextgeneration sequencing technologies
    • Zhang W, Chen J, Yang Y, et al. A practical comparison of de novo genome assembly software tools for nextgeneration sequencing technologies. PLoS ONE 2011;6: e17915.
    • (2011) PLoS ONE , vol.6
    • Zhang, W.1    Chen, J.2    Yang, Y.3
  • 27
    • 54949137701 scopus 로고    scopus 로고
    • MetaSim: a sequencing simulator for genomics and metagenomics
    • Richter DC, Ott F, Auch AF, et al. MetaSim: a sequencing simulator for genomics and metagenomics. PLoS ONE 2008;3:e3373.
    • (2008) PLoS ONE , vol.3
    • Richter, D.C.1    Ott, F.2    Auch, A.F.3
  • 28
    • 0033555906 scopus 로고    scopus 로고
    • Tandem repeats finder: a program to analyze DNA sequences
    • Benson G. Tandem repeats finder: a program to analyze DNA sequences. Nucleic Acids Res 1999;27:573-80.
    • (1999) Nucleic Acids Res , vol.27 , pp. 573-580
    • Benson, G.1
  • 29
    • 0036226603 scopus 로고    scopus 로고
    • BLAT-the BLAST-like alignment tool
    • Kent WJ. BLAT-the BLAST-like alignment tool. Genome Res 2002;12:656-64.
    • (2002) Genome Res , vol.12 , pp. 656-664
    • Kent, W.J.1
  • 30
    • 77951813504 scopus 로고    scopus 로고
    • Genome assembly quality: assessment and improvement using the neutral indel model
    • Meader S, Hillier LW, Locke D, et al. Genome assembly quality: assessment and improvement using the neutral indel model. Genome Res 2010;20:675-84.
    • (2010) Genome Res , vol.20 , pp. 675-684
    • Meader, S.1    Hillier, L.W.2    Locke, D.3
  • 31
    • 76749117156 scopus 로고    scopus 로고
    • Assembly complexity of prokaryotic genomes using short reads
    • Kingsford C, Schatz MC, Pop M. Assembly complexity of prokaryotic genomes using short reads. BMC Bioinformatics 2010;11:21.
    • (2010) BMC Bioinformatics , vol.11 , pp. 21
    • Kingsford, C.1    Schatz, M.C.2    Pop, M.3
  • 32
    • 79953854485 scopus 로고    scopus 로고
    • Assessing the benefits of using mate-pairs to resolve repeats in de novo short-read prokaryotic assemblies
    • Wetzel J, Kingsford C, Pop M. Assessing the benefits of using mate-pairs to resolve repeats in de novo short-read prokaryotic assemblies. BMC Bioinformatics 2011;12:95.
    • (2011) BMC Bioinformatics , vol.12 , pp. 95
    • Wetzel, J.1    Kingsford, C.2    Pop, M.3
  • 33
    • 0033533089 scopus 로고    scopus 로고
    • The origin of eukaryotes: the difference between prokaryotic and eukaryotic cells
    • Vellai T, Vida G. The origin of eukaryotes: the difference between prokaryotic and eukaryotic cells. Proc RSoc Lond B Biol Sci 1999;266:1571-7.
    • (1999) Proc RSoc Lond B Biol Sci , vol.266 , pp. 1571-1577
    • Vellai, T.1    Vida, G.2
  • 34
    • 31044448817 scopus 로고    scopus 로고
    • Evolutionary change-patterns and processes
    • Salzano FM. Evolutionary change-patterns and processes. An Acad Bras Cienc 2005;77:627-50.
    • (2005) An Acad Bras Cienc , vol.77 , pp. 627-650
    • Salzano, F.M.1
  • 35
    • 77952886150 scopus 로고    scopus 로고
    • Assembly algorithms for next-generation sequencing data
    • Miller JR, Koren S, Sutton G. Assembly algorithms for next-generation sequencing data. Genomics 2010;95: 315-27.
    • (2010) Genomics , vol.95 , pp. 315-327
    • Miller, J.R.1    Koren, S.2    Sutton, G.3
  • 36
    • 79960411408 scopus 로고    scopus 로고
    • Comparative studies of de novo assembly tools for next-generation sequencing technologies
    • Lin Y, Li J, Shen H, et al. Comparative studies of de novo assembly tools for next-generation sequencing technologies. Bioinformatics 2011;27:2031-7.
    • (2011) Bioinformatics , vol.27 , pp. 2031-2037
    • Lin, Y.1    Li, J.2    Shen, H.3
  • 37
    • 77955385735 scopus 로고    scopus 로고
    • Read length and repeat resolution: exploring prokaryote genomes using next-generation sequencing technologies
    • Cahill MJ, Koser CU, Ross NE, et al. Read length and repeat resolution: exploring prokaryote genomes using next-generation sequencing technologies. PLoS ONE 2010;5:e11518.
    • (2010) PLoS ONE , vol.5
    • Cahill, M.J.1    Koser, C.U.2    Ross, N.E.3
  • 38
    • 41249098849 scopus 로고    scopus 로고
    • A high quality draft consensus sequence of the genome of a heterozygous grapevine variety
    • Velasco R, Zharkikh A, Troggio M, et al. A high quality draft consensus sequence of the genome of a heterozygous grapevine variety. PLoS One 2007;2:e1326.
    • (2007) PLoS One , vol.2
    • Velasco, R.1    Zharkikh, A.2    Troggio, M.3
  • 39
    • 77957560949 scopus 로고    scopus 로고
    • The genome of the domesticated apple (Malus x domestica Borkh)
    • Velasco R, Zharkikh A, Affourtit J, etal. The genome of the domesticated apple (Malus x domestica Borkh.). Nat Genet 2010;42:833-839.
    • (2010) Nat Genet , vol.42 , pp. 833-839
    • Velasco, R.1    Zharkikh, A.2    Affourtit, J.3


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.