메뉴 건너뛰기




Volumn 27, Issue 3, 2011, Pages 295-302

HiTEC: Accurate error correction in high-throughput sequencing data

Author keywords

[No Author keywords available]

Indexed keywords

ALGORITHM; ARTICLE; BIOLOGICAL MODEL; COMPUTER PROGRAM; DNA SEQUENCE; GENOME; METHODOLOGY; REPRODUCIBILITY;

EID: 79551589417     PISSN: 13674803     EISSN: 14602059     Source Type: Journal    
DOI: 10.1093/bioinformatics/btq653     Document Type: Article
Times cited : (104)

References (36)
  • 1
    • 43149086380 scopus 로고    scopus 로고
    • ALLPATHS: De novo assembly of whole-genome shotgun microreads
    • Butler,J. et al. (2008) ALLPATHS: De novo assembly of whole-genome shotgun microreads. Genome Res., 18, 810-820.
    • (2008) Genome Res. , vol.18 , pp. 810-820
    • Butler, J.1
  • 2
    • 63549114801 scopus 로고    scopus 로고
    • PASS: a program to align short sequences
    • Campagna,D. et al. (2009) PASS: a program to align short sequences. Bioinformatics, 25, 967-968.
    • (2009) Bioinformatics , vol.25 , pp. 967-968
    • Campagna, D.1
  • 3
    • 59949093527 scopus 로고    scopus 로고
    • De novo fragment assembly with short mate-paired reads: Does the read length matter?
    • Chaisson,M.J. et al. (2009) De novo fragment assembly with short mate-paired reads: Does the read length matter?. Genome Res., 19, 336-346.
    • (2009) Genome Res. , vol.19 , pp. 336-346
    • Chaisson, M.J.1
  • 4
    • 47249091503 scopus 로고    scopus 로고
    • Assembly for double-ended short-read sequencing technologies
    • Mardis,E. et al. (eds), Artech House Publishers, New York
    • Chen,J. and Skiena,S. (2007) Assembly for double-ended short-read sequencing technologies. In Mardis,E. et al. (eds) Advances in Genome Sequencing Technology and Algorithms, Artech House Publishers, New York, pp. 123-141.
    • (2007) Advances in Genome Sequencing Technology and Algorithms , pp. 123-141
    • Chen, J.1    Skiena, S.2
  • 5
    • 70349886587 scopus 로고    scopus 로고
    • PerM: efficient mapping of short sequencing reads with periodic full sensitive spaced seeds
    • Chen,Y. (2009) PerM: efficient mapping of short sequencing reads with periodic full sensitive spaced seeds. Bioinformatics, 25, 2514-2521.
    • (2009) Bioinformatics , vol.25 , pp. 2514-2521
    • Chen, Y.1
  • 6
    • 35948929094 scopus 로고    scopus 로고
    • SHARCGS, a fast and highly accurate short-read assembly algorithm for de novo genomic sequencing
    • Dohm,J.C. et al. (2007) SHARCGS, a fast and highly accurate short-read assembly algorithm for de novo genomic sequencing. Genome Res., 17, 1697-1706.
    • (2007) Genome Res. , vol.17 , pp. 1697-1706
    • Dohm, J.C.1
  • 7
    • 63549110603 scopus 로고    scopus 로고
    • MOM: maximum oligonucleotide mapping
    • Eaves,L.H. and Gao,Y. (2009) MOM: maximum oligonucleotide mapping. Bioinformatics, 25, 969-970.
    • (2009) Bioinformatics , vol.25 , pp. 969-970
    • Eaves, L.H.1    Gao, Y.2
  • 8
    • 43149085041 scopus 로고    scopus 로고
    • De novo bacterial genome sequencing: millions of very short reads assembled on a desktop computer
    • Hernandez,D. et al. (2008) De novo bacterial genome sequencing: millions of very short reads assembled on a desktop computer. Genome Res., 18, 802-809.
    • (2008) Genome Res. , vol.18 , pp. 802-809
    • Hernandez, D.1
  • 9
    • 36448948250 scopus 로고    scopus 로고
    • Extending assembly of short DNA sequences to handle error
    • Jeck,W.R. et al. (2007) Extending assembly of short DNA sequences to handle error. Bioinformatics, 23, 2942-2944.
    • (2007) Bioinformatics , vol.23 , pp. 2942-2944
    • Jeck, W.R.1
  • 10
    • 53749083993 scopus 로고    scopus 로고
    • SeqMap: mapping massive amount of oligonucleotides to the genome
    • Jiang,H. andWong,W.H (2008) SeqMap: mapping massive amount of oligonucleotides to the genome. Bioinformatics, 24, 2395-2396.
    • (2008) Bioinformatics , vol.24 , pp. 2395-2396
    • Jiang, H.1    Wong, W.H.2
  • 11
    • 65649116903 scopus 로고    scopus 로고
    • ProbeMatch: a tool for aligning oligonucleotide sequences
    • Jung Kim,Y. et al. (2009) ProbeMatch: a tool for aligning oligonucleotide sequences. Bioinformatics, 25, 1424-1425.
    • (2009) Bioinformatics , vol.25 , pp. 1424-1425
    • Jung Kim, Y.1
  • 13
    • 84956976999 scopus 로고    scopus 로고
    • Linear-time longest-common-prefix computation in suffix arrays and its applications
    • Springer, Berlin
    • Kasai,T. et al. (2001) Linear-time longest-common-prefix computation in suffix arrays and its applications. In Proceedings of CPM'01, Vol. 2089 of Lecture Notes in Computer Science, Springer, Berlin, pp. 181-192.
    • (2001) Proceedings of CPM'01, of Lecture Notes in Computer Science , vol.2089 , pp. 181-192
    • Kasai, T.1
  • 14
    • 18544373057 scopus 로고    scopus 로고
    • Constructing suffix arrays in linear time
    • Kim,D.K. et al. (2005) Constructing suffix arrays in linear time. J. Discrete Algorithms, 3, 126-142.
    • (2005) J. Discrete Algorithms , vol.3 , pp. 126-142
    • Kim, D.K.1
  • 15
    • 18544364760 scopus 로고    scopus 로고
    • Space efficient linear time construction of suffix arrays
    • Ko,P. and Aluru,S. (2005) Space efficient linear time construction of suffix arrays. J. Discrete Algorithms, 3, 143-156.
    • (2005) J. Discrete Algorithms , vol.3 , pp. 143-156
    • Ko, P.1    Aluru, S.2
  • 16
    • 62349130698 scopus 로고    scopus 로고
    • Ultrafast and memory-efficient alignment of short DNA sequences to the human genome
    • Langmead,B. et al. (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
  • 17
    • 55549097836 scopus 로고    scopus 로고
    • Mapping short DNA sequencing reads and calling variants using mapping quality scores
    • Li,H. et al. (2008a) 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
  • 18
    • 40049104732 scopus 로고    scopus 로고
    • SOAP: short oligonucleotide alignment program
    • Li,R. et al. (2008b) SOAP: short oligonucleotide alignment program. Bioinformatics, 24, 713-714.
    • (2008) Bioinformatics , vol.24 , pp. 713-714
    • Li, R.1
  • 19
    • 67649884743 scopus 로고    scopus 로고
    • Fast and accurate short read alignment with Burrows-Wheeler transform
    • Li,H. and Durbin,R. (2009) Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics, 25, 1754-1760.
    • (2009) Bioinformatics , vol.25 , pp. 1754-1760
    • Li, H.1    Durbin, R.2
  • 20
    • 54949110994 scopus 로고    scopus 로고
    • ZOOM! Zillions of oligos mapped
    • Lin,H. et al. (2008) ZOOM! Zillions of oligos mapped. Bioinformatics, 24, 2431-2437.
    • (2008) Bioinformatics , vol.24 , pp. 2431-2437
    • Lin, H.1
  • 21
    • 58049195681 scopus 로고    scopus 로고
    • Slider-maximum use of probability information for alignment of short sequence reads and SNP detection
    • Malhis,N. et al. (2009) Slider-maximum use of probability information for alignment of short sequence reads and SNP detection. Bioinformatics, 25, 6-13.
    • (2009) Bioinformatics , vol.25 , pp. 6-13
    • Malhis, N.1
  • 22
    • 0027681165 scopus 로고
    • Suffix arrays: a new method for on-line search
    • Manber,U. and Myers,G. (1993) Suffix arrays: a new method for on-line search. SIAM J. Comput., 22, 935-948.
    • (1993) SIAM J. Comput. , vol.22 , pp. 935-948
    • Manber, U.1    Myers, G.2
  • 23
    • 39649117755 scopus 로고    scopus 로고
    • The impact of next-generation sequencing technology on genetics
    • Mardis,E.R. (2008) The impact of next-generation sequencing technology on genetics. Trends Genet., 24, 133-141.
    • (2008) Trends Genet. , vol.24 , pp. 133-141
    • Mardis, E.R.1
  • 24
    • 27544497879 scopus 로고    scopus 로고
    • Building fragment assembly string graphs
    • Myers,G. (2005) Building fragment assembly string graphs. Bioinformatics, 21, ii79-ii85.
    • (2005) Bioinformatics , vol.21
    • Myers, G.1
  • 25
    • 67049159825 scopus 로고    scopus 로고
    • SHRiMP: accurate mapping of short color-space reads
    • Rumble,S.M. et al. (2009) SHRiMP: accurate mapping of short color-space reads. PLoS Comput. Biol., 5, e1000386.
    • (2009) PLoS Comput. Biol. , vol.5
    • Rumble, S.M.1
  • 26
    • 77952857079 scopus 로고    scopus 로고
    • Correction of sequencing errors in a mixed set of reads
    • Salmela,L. (2010) Correction of sequencing errors in a mixed set of reads. Bioinformatics, 26, 1284-1290.
    • (2010) Bioinformatics , vol.26 , pp. 1284-1290
    • Salmela, L.1
  • 27
    • 0017681196 scopus 로고
    • DNA sequencing with chain-terminating inhibitors
    • Sanger,F. et al. (1977) DNA sequencing with chain-terminating inhibitors. Proc. Natl Acad. Sci. USA, 74, 5463-5467.
    • (1977) Proc. Natl Acad. Sci. USA , vol.74 , pp. 5463-5467
    • Sanger, F.1
  • 28
    • 65649120715 scopus 로고    scopus 로고
    • Cloudburst: highly sensitive read mapping with mapreduce
    • Schatz,M. (2009) Cloudburst: highly sensitive read mapping with mapreduce. Bioinformatics, 25, 1363-1369.
    • (2009) Bioinformatics , vol.25 , pp. 1363-1369
    • Schatz, M.1
  • 29
    • 69949178009 scopus 로고    scopus 로고
    • SHREC: a short-read error correction method
    • Schroder,J. et al. (2009) SHREC: a short-read error correction method. Bioinformatics, 25, 2157-2163.
    • (2009) Bioinformatics , vol.25 , pp. 2157-2163
    • Schroder, J.1
  • 30
    • 77952001158 scopus 로고    scopus 로고
    • A parallel algorithm for error correction in high-throughput shortread data on CUDA-enabled graphics hardware
    • Shi,H. et al. (2010) A parallel algorithm for error correction in high-throughput shortread data on CUDA-enabled graphics hardware. J. Comput. Biol., 17, 603-615.
    • (2010) J. Comput. Biol. , vol.17 , pp. 603-615
    • Shi, H.1
  • 31
    • 66449136667 scopus 로고    scopus 로고
    • ABySS: a parallel assembler for short read sequence data
    • Simpson,J.T. et al. (2009) ABySS: a parallel assembler for short read sequence data. Genome Res., 19, 1117-1123.
    • (2009) Genome Res. , vol.19 , pp. 1117-1123
    • Simpson, J.T.1
  • 32
    • 41249096306 scopus 로고    scopus 로고
    • Using quality scores and longer reads improves accuracy of Solexa read mapping
    • Smith,A.D. et al. (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
  • 33
    • 33847307402 scopus 로고    scopus 로고
    • Assembling millions of short DNAsequences using SSAKE
    • Warren,R.Rl. et al. (2007)Assembling millions of short DNAsequences using SSAKE. Bioinformatics, 23, 500-501.
    • (2007) Bioinformatics , vol.23 , pp. 500-501
    • Warren, R.Rl.1
  • 34
    • 77957758142 scopus 로고    scopus 로고
    • Reptile: representative tiling for short read error correction
    • Yang,X. et al. (2010) Reptile: representative tiling for short read error correction. Bioinformatics, 26, 2526-2533.
    • (2010) Bioinformatics , vol.26 , pp. 2526-2533
    • Yang, X.1
  • 35
    • 43149115851 scopus 로고    scopus 로고
    • Velvet: algorithms for de novo short read assembly using De Bruijn graphs
    • Zerbino,D. and Birney,E. (2008) Velvet: algorithms for de novo short read assembly using De Bruijn graphs. Genome Res., 18, 821-829.
    • (2008) Genome Res. , vol.18 , pp. 821-829
    • Zerbino, D.1    Birney, E.2
  • 36
    • 76649119779 scopus 로고    scopus 로고
    • The next-generation sequencing technology: a technology review and future perspective
    • Zhou,X. et al. (2010) The next-generation sequencing technology: a technology review and future perspective. Sci. China, 53, 44-57.
    • (2010) Sci. China , vol.53 , pp. 44-57
    • Zhou, X.1


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.