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Volumn 9, Issue 1, 2014, Pages

CUSHAW3: Sensitive and accurate base-space and color-space short-read alignment with hybrid seeding

Author keywords

[No Author keywords available]

Indexed keywords

ANALYTICAL ERROR; ARTICLE; COMPUTER PROGRAM; CONTROLLED STUDY; GENETIC PROCEDURES; HUMAN; HUMAN GENOME; HYBRID SEEDING; INTERMETHOD COMPARISON; INTERNET; NEXT GENERATION SEQUENCING; SENSITIVITY ANALYSIS; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS; SIMULATION; STATISTICAL PARAMETERS;

EID: 84899539925     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0086869     Document Type: Article
Times cited : (43)

References (26)
  • 1
    • 41249096306 scopus 로고    scopus 로고
    • Using quality scores and longer reads improves accuracy of Solexa read mapping
    • Smith AD, Xuan Z, Zhang MQ (2008) Using quality scores and longer reads improves accuracy of Solexa read mapping. BMC Bioinformatics, 9: 128.
    • (2008) BMC Bioinformatics , vol.9 , pp. 128
    • Smith, A.D.1    Xuan, Z.2    Zhang, M.Q.3
  • 2
    • 55549097836 scopus 로고    scopus 로고
    • Mapping short DNA sequencing reads and calling variants using mapping quality scores
    • Li H, Ruan J, Durbin R (2008) Mapping short DNA sequencing reads and calling variants using mapping quality scores. Genome Res., 18: 1851-1858.
    • (2008) Genome Res. , vol.18 , pp. 1851-1858
    • Li, H.1    Ruan, J.2    Durbin, R.3
  • 3
    • 70450177746 scopus 로고    scopus 로고
    • BFAST: An alignment tool for large scale genome resequencing
    • Homer N, Merriman B, Nelson SF (2009) BFAST: an alignment tool for large scale genome resequencing. Plos One, 4: e7767.
    • (2009) Plos One , vol.4
    • Homer, N.1    Merriman, B.2    Nelson, S.F.3
  • 4
    • 62349130698 scopus 로고    scopus 로고
    • Ultrafast and memory-efficient alignment of short DNA sequences to the human genome
    • Langmead B, Trapnell C, Pop M, Salzberg SL (2009) Ultrafast and memory-efficient 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.L.4
  • 5
    • 67649884743 scopus 로고    scopus 로고
    • Fast and accurate short read alignment with Burrows-Wheeler transform
    • Li H, Durbin R (2009) Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics, 25: 1755-1760.
    • (2009) Bioinformatics , vol.25 , pp. 1755-1760
    • Li, H.1    Durbin, R.2
  • 6
    • 84864136658 scopus 로고    scopus 로고
    • CUSHAW: A CUDA compatible short read aligner to large genomes based on the Burrows-Wheeler transform
    • Liu Y, Schmidt B, Maskell DL (2012) CUSHAW: a CUDA compatible short read aligner to large genomes based on the Burrows-Wheeler transform. Bioinformatics, 28: 1830-1837.
    • (2012) Bioinformatics , vol.28 , pp. 1830-1837
    • Liu, Y.1    Schmidt, B.2    Maskell, D.L.3
  • 7
    • 84859048351 scopus 로고    scopus 로고
    • SOAP3: Ultra-fast GPU-based parallel alignment tool for short reads
    • Liu CM, Wong T, Wu E, Luo R, Yiu SM, et al. (2012) SOAP3: ultra-fast GPU-based parallel alignment tool for short reads. Bioinformatics, 28: 878-879.
    • (2012) Bioinformatics , vol.28 , pp. 878-879
    • Liu, C.M.1    Wong, T.2    Wu, E.3    Luo, R.4    Yiu, S.M.5
  • 8
    • 77949587649 scopus 로고    scopus 로고
    • Fast and accurate long-read alignment with Burrows-Wheeler transform
    • Li H, Durbin R (2010) Fast and accurate long-read alignment with Burrows-Wheeler transform. Bioinformatics, 26: 589-595.
    • (2010) Bioinformatics , vol.26 , pp. 589-595
    • Li, H.1    Durbin, R.2
  • 9
    • 77957815609 scopus 로고    scopus 로고
    • GASSST: Global alignment short sequence search tool
    • Rizk G, Lavenier D (2010) GASSST: global alignment short sequence search tool. Bioinformatics, 26: 2534-2540.
    • (2010) Bioinformatics , vol.26 , pp. 2534-2540
    • Rizk, G.1    Lavenier, D.2
  • 10
    • 84859210032 scopus 로고    scopus 로고
    • Fast gapped-read alignment with Bowtie 2
    • Langmead B, Salzberg S (2012) Fast gapped-read alignment with Bowtie 2. Nature Methods, 9: 357-359.
    • (2012) Nature Methods , vol.9 , pp. 357-359
    • Langmead, B.1    Salzberg, S.2
  • 11
    • 84866447703 scopus 로고    scopus 로고
    • Long read alignment based on maximal exact match seeds
    • Liu Y, Schmidt B (2012) Long read alignment based on maximal exact match seeds. Bioinformatics, 28, i318-i324.
    • (2012) Bioinformatics , vol.28
    • Liu, Y.1    Schmidt, B.2
  • 12
    • 84870837088 scopus 로고    scopus 로고
    • The GEM mapper: Fast, accurate and versatile alignment by filtration
    • Marco-Sola S, Sammeth M, Guigó R, Ribeca P (2012) The GEM mapper: fast, accurate and versatile alignment by filtration. Nature Methods, 9: 1885-1888.
    • (2012) Nature Methods , vol.9 , pp. 1885-1888
    • Marco-Sola, S.1    Sammeth, M.2    Guigó, R.3    Ribeca, P.4
  • 14
    • 84878532952 scopus 로고    scopus 로고
    • SOAP3-dp: Fast, accurate and sensitive GPU-based short-read aligner
    • Luo R, Wong T, Zhu J, Liu CM, Zhu X, et al. (2013) SOAP3-dp: fast, accurate and sensitive GPU-based short-read aligner. PLOS One, 8: e65632.
    • (2013) PLOS One , vol.8
    • Luo, R.1    Wong, T.2    Zhu, J.3    Liu, C.M.4    Zhu, X.5
  • 16
    • 77957272611 scopus 로고    scopus 로고
    • A survey of sequence alignment algorithms for next-generation sequencing
    • Li H, Homer N (2010) A survey of sequence alignment algorithms for next-generation sequencing. Brief Bioinform., 11: 473-483.
    • (2010) Brief Bioinform. , vol.11 , pp. 473-483
    • Li, H.1    Homer, N.2
  • 17
    • 79956307251 scopus 로고    scopus 로고
    • Stampy: A statistical algorithm for sensitive and fast mapping of Illumina sequence reads
    • Lunter G, Goodson M (2011) Stampy: a statistical algorithm for sensitive and fast mapping of Illumina sequence reads. Genome Res., 21: 936-939.
    • (2011) Genome Res. , vol.21 , pp. 936-939
    • Lunter, G.1    Goodson, M.2
  • 18
    • 0034764307 scopus 로고    scopus 로고
    • SSAHA: A fast search method for large DNA databases
    • DOI 10.1101/gr.194201
    • Ning Z, Cox AJ, Mullikin JC (2001) SSAHA: a fast search method for large DNA databases. Genome Res., 11: 1725-1729. (Pubitemid 33040499)
    • (2001) Genome Research , vol.11 , Issue.10 , pp. 1725-1729
    • Ning, Z.1    Cox, A.J.2    Mullikin, J.C.3
  • 21
    • 84857145150 scopus 로고    scopus 로고
    • ART: A next-generation sequencing read simulator
    • Huang W, Li L, Myers JR, Marth GT (2012) ART: a next-generation sequencing read simulator. Bioinformatics, 28: 593-594.
    • (2012) Bioinformatics , vol.28 , pp. 593-594
    • Huang, W.1    Li, L.2    Myers, J.R.3    Marth, G.T.4
  • 22
    • 0031978181 scopus 로고    scopus 로고
    • Base-calling of automated sequencer traces using phred. II. Error probabilities
    • Ewing B, Green P (1998) Base-calling of automated sequencer traces using phred. II. Error probabilities. Genome Res 8: 186-194. (Pubitemid 28177230)
    • (1998) Genome Research , vol.8 , Issue.3 , pp. 186-194
    • Ewing, B.1    Green, P.2
  • 23
    • 77956295988 scopus 로고    scopus 로고
    • The Genome Analysis Toolkit: A MapReduce framework for analyzing next generation DNA sequencing data
    • McKenna A, Hanna M, Banks E, Sivachenko A, Cibulskis K, et al. (2010) The Genome Analysis Toolkit: a MapReduce framework for analyzing next generation DNA sequencing data. Genome Res 20: 1297-1303.
    • (2010) Genome Res , vol.20 , pp. 1297-1303
    • McKenna, A.1    Hanna, M.2    Banks, E.3    Sivachenko, A.4    Cibulskis, K.5
  • 26
    • 0019887799 scopus 로고
    • Identification of common molecular subsequences
    • Smith TF, Waterman MS (1981) Identification of common molecular subsequences. J. Mol. Biol., 147: 195-197.
    • (1981) J. Mol. Biol. , vol.147 , pp. 195-197
    • Smith, T.F.1    Waterman, M.S.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.