메뉴 건너뛰기




Volumn 14, Issue , 2013, Pages

Sequencing error correction without a reference genome

Author keywords

[No Author keywords available]

Indexed keywords

COMPLEX EFFECTS; ERROR MODEL; ERROR PROBABILITIES; ERROR RATE; MICRORNAS; RNA EDITING; SEQUENCING ERRORS; ULTRA DEEPS;

EID: 84890386468     PISSN: None     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/1471-2105-14-367     Document Type: Article
Times cited : (21)

References (18)
  • 1
    • 79959829720 scopus 로고    scopus 로고
    • Widespread RNA and DNA sequence differences in the human transcriptome
    • 10.1126/science.1207018, 3204392, 21596952
    • Li M, Wang IX, Li Y, Bruzel A, Richards AL, Toung JM, Cheung VG. Widespread RNA and DNA sequence differences in the human transcriptome. Science 2011, 333(6038):53-58. 10.1126/science.1207018, 3204392, 21596952.
    • (2011) Science , vol.333 , Issue.6038 , pp. 53-58
    • Li, M.1    Wang, I.X.2    Li, Y.3    Bruzel, A.4    Richards, A.L.5    Toung, J.M.6    Cheung, V.G.7
  • 2
    • 84858328300 scopus 로고
    • Comment on 'Widespread RNA and DNA sequence differences in the human transcriptome'?
    • Pickrell JK, Gilad Y, Pritchard JK. Comment on 'Widespread RNA and DNA sequence differences in the human transcriptome'?. Science 1302, 335(6074).
    • (1302) Science , vol.335 , Issue.6074
    • Pickrell, J.K.1    Gilad, Y.2    Pritchard, J.K.3
  • 3
    • 69949135779 scopus 로고    scopus 로고
    • Swift: primary data analysis for the Illumina Solexa sequencing platform
    • 10.1093/bioinformatics/btp383, 2734321, 19549630
    • Whiteford N, Skelly T, Curtis C, Ritchie ME, Löhr A, Zaranek AW, Abnizova I, Brown C. Swift: primary data analysis for the Illumina Solexa sequencing platform. Bioinformatics 2009, 25(17):2194-2199. 10.1093/bioinformatics/btp383, 2734321, 19549630.
    • (2009) Bioinformatics , vol.25 , Issue.17 , pp. 2194-2199
    • Whiteford, N.1    Skelly, T.2    Curtis, C.3    Ritchie, M.E.4    Löhr, A.5    Zaranek, A.W.6    Abnizova, I.7    Brown, C.8
  • 4
    • 0033062766 scopus 로고    scopus 로고
    • An estimate of the crosstalk matrix in four-dye fluorescence-based DNA sequencing
    • Li L, Speed T. An estimate of the crosstalk matrix in four-dye fluorescence-based DNA sequencing. Electrophoresis 1999, 20:1522-2683.
    • (1999) Electrophoresis , vol.20 , pp. 1522-2683
    • Li, L.1    Speed, T.2
  • 5
    • 80053194792 scopus 로고    scopus 로고
    • Base-calling for next-generation sequencing platforms
    • 10.1093/bib/bbq077, 3178052, 21245079
    • Ledergerber C, Dessimoz C. Base-calling for next-generation sequencing platforms. Brief Bioinform 2011, 12(5):489-497. 10.1093/bib/bbq077, 3178052, 21245079.
    • (2011) Brief Bioinform , vol.12 , Issue.5 , pp. 489-497
    • Ledergerber, C.1    Dessimoz, C.2
  • 7
    • 52649157765 scopus 로고    scopus 로고
    • Substantial biases in ultra-short read data sets from high-throughput DNA sequencing
    • 10.1093/nar/gkn425, 2532726, 18660515
    • 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. 10.1093/nar/gkn425, 2532726, 18660515.
    • (2008) Nucleic Acids Res , vol.36 , Issue.16
    • Dohm, J.C.1    Lottaz, C.2    Borodina, T.3    Himmelbauer, H.4
  • 8
    • 84865992574 scopus 로고    scopus 로고
    • A survey of error-correction methods for next-generation sequencing
    • 10.1093/bib/bbs015, 22492192
    • Yang X, Chockalingam SP, Aluru S. A survey of error-correction methods for next-generation sequencing. Brief Bioinformatics 2013, 14:56-66. 10.1093/bib/bbs015, 22492192.
    • (2013) Brief Bioinformatics , vol.14 , pp. 56-66
    • Yang, X.1    Chockalingam, S.P.2    Aluru, S.3
  • 9
    • 69949178009 scopus 로고    scopus 로고
    • SHREC a short-read error correction method
    • 10.1093/bioinformatics/btp379, 19542152
    • Schröder J, Schröder H, Puglisi SJ, Sinha R, Schmidt B. SHREC a short-read error correction method. Bioinformatics 2009, 25(17):2157-2163. 10.1093/bioinformatics/btp379, 19542152.
    • (2009) Bioinformatics , vol.25 , Issue.17 , pp. 2157-2163
    • Schröder, J.1    Schröder, H.2    Puglisi, S.J.3    Sinha, R.4    Schmidt, B.5
  • 10
    • 79551589417 scopus 로고    scopus 로고
    • HiTEC: accurate error correction in high-throughput sequencing data
    • 10.1093/bioinformatics/btq653, 21115437
    • Ilie L, Fazayeli F, Ilie S. HiTEC: accurate error correction in high-throughput sequencing data. Bioinformatics 2011, 27(3):295-302. 10.1093/bioinformatics/btq653, 21115437.
    • (2011) Bioinformatics , vol.27 , Issue.3 , pp. 295-302
    • Ilie, L.1    Fazayeli, F.2    Ilie, S.3
  • 11
    • 79951539256 scopus 로고    scopus 로고
    • Repeat-aware modeling and correction of short read errors
    • 10.1186/1471-2105-12-S1-S52, 3044310, 21342585
    • Yang X, Aluru S, Dorman K. Repeat-aware modeling and correction of short read errors. BMC Bioinformatics 2011, 12(Suppl 1):S52. 10.1186/1471-2105-12-S1-S52, 3044310, 21342585.
    • (2011) BMC Bioinformatics , vol.12 , Issue.SUPPL. 1
    • Yang, X.1    Aluru, S.2    Dorman, K.3
  • 12
    • 77952973011 scopus 로고    scopus 로고
    • Recount: expectation maximization based error correction tool for next generation sequencing data
    • Wijaya E, Frith MC, Suzuki Y, Horton P. Recount: expectation maximization based error correction tool for next generation sequencing data. In Genome Inform 2009, 23:189-201.
    • (2009) In Genome Inform , vol.23 , pp. 189-201
    • Wijaya, E.1    Frith, M.C.2    Suzuki, Y.3    Horton, P.4
  • 13
    • 67650074197 scopus 로고    scopus 로고
    • Efficient frequency-based de novo short-read clustering for error trimming in next-generation sequencing
    • 10.1101/gr.089151.108, 2704438, 19439514, Hashimoto S i
    • Qu W, Morishita S, Hashimoto S i Efficient frequency-based de novo short-read clustering for error trimming in next-generation sequencing. Genome Res 2009, 19(7):1309-1315. 10.1101/gr.089151.108, 2704438, 19439514, Hashimoto S i.
    • (2009) Genome Res , vol.19 , Issue.7 , pp. 1309-1315
    • Qu, W.1    Morishita, S.2
  • 14
    • 79951958731 scopus 로고    scopus 로고
    • Discovery of barley miRNAs through deep sequencing of short reads
    • 10.1186/1471-2164-12-129, 3060140, 21352554
    • Schreiber A, Shi BJ, Huang CY, Langridge P, Baumann U. Discovery of barley miRNAs through deep sequencing of short reads. BMC Genomics 2011, 12:129. 10.1186/1471-2164-12-129, 3060140, 21352554.
    • (2011) BMC Genomics , vol.12 , pp. 129
    • Schreiber, A.1    Shi, B.J.2    Huang, C.Y.3    Langridge, P.4    Baumann, U.5
  • 15
    • 85081456309 scopus 로고    scopus 로고
    • Source code for sequencing error correction without a reference genome
    • Source code for sequencing error correction without a reference genome. [http://unisa.edu.au/Research/Phenomics-and-Bioinformatics-Research-Centre/Software/].
  • 16
    • 70350023532 scopus 로고    scopus 로고
    • Improved base calling for the Illumina Genome Analyzer using machine learning strategies
    • 10.1186/gb-2009-10-8-r83, 2745764, 19682367
    • Kircher M, Stenzel U, Kelso J. Improved base calling for the Illumina Genome Analyzer using machine learning strategies. Genome Biol 2009, 10(8):R83+. 10.1186/gb-2009-10-8-r83, 2745764, 19682367.
    • (2009) Genome Biol , vol.10 , Issue.8
    • Kircher, M.1    Stenzel, U.2    Kelso, J.3
  • 17
    • 80455126001 scopus 로고    scopus 로고
    • Evaluation of genomic high-throughput sequencing data generated on illumina HiSeq and genome analyzer systems
    • 10.1186/gb-2011-12-11-r112, 3334598, 22067484
    • Minoche A, Dohm J, Himmelbauer H. Evaluation of genomic high-throughput sequencing data generated on illumina HiSeq and genome analyzer systems. Genome Biol 2011, 12(11):R112. 10.1186/gb-2011-12-11-r112, 3334598, 22067484.
    • (2011) Genome Biol , vol.12 , Issue.11
    • Minoche, A.1    Dohm, J.2    Himmelbauer, H.3
  • 18
    • 85081458330 scopus 로고    scopus 로고
    • Illumina IGenomes collection
    • Illumina IGenomes collection. [http://support.illumina.com/sequencing/sequencing_software/igenome.ilmn].


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.