Sequence-specific error profile of Illumina sequencers

Nucleic Acids Research

Volumn 39, Issue 13, 2011, Pages

  Nakamura, Kensuke ^a   Oshima, Taku ^b   Morimoto, Takuya ^b,c   Ikeda, Shun ^a   Yoshikawa, Hirofumi ^d   Shiwa, Yuh ^d   Ishikawa, Shu ^b   Linak, Margaret C ^e   Hirai, Aki ^a   Takahashi, Hiroki ^a   Altaf Ul Amin, Md ^a   Ogasawara, Naotake ^b   Kanaya, Shigehiko ^a  

^a Graduate Sch of Information Science   (Japan)

^b NARA INSTITUTE OF SCIENCE AND TECHNOLOGY   (Japan)

^c KAO CORPORATION   (Japan)

^d TOKYO UNIVERSITY OF AGRICULTURE   (Japan)

^e UNIVERSITY OF MINNESOTA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

CYTOSINE; GUANINE; SINGLE STRANDED DNA;

ANALYTICAL ERROR; ARTICLE; BACILLUS SUBTILIS; BORDETELLA PERTUSSIS; COMPUTER PROGRAM; CONTROLLED STUDY; DNA SEQUENCE; GENE MAPPING; INVERTED REPEAT; MYCOBACTERIUM BOVIS; NONHUMAN; NUCLEOTIDE SEQUENCE; POPULATION GENETICS; PRIORITY JOURNAL; PROTEIN ASSEMBLY; PROTEIN DNA INTERACTION; PROTEIN FOLDING; RNA SEQUENCE; SEQUENCE ANALYSIS; SEQUENCE SPECIFIC ERROR; SINGLE NUCLEOTIDE POLYMORPHISM; STAPHYLOCOCCUS AUREUS;

BACILLUS SUBTILIS; BASE PAIR MISMATCH; CHROMOSOME MAPPING; GENOME, BACTERIAL; INVERTED REPEAT SEQUENCES; SEQUENCE ANALYSIS, DNA; SEQUENCE ANALYSIS, RNA;

EID: 80052226692     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkr344     Document Type: Article

References (39)

1. Quail, M.A., Kozarewa, I., Smith, F., Scally, A., Stephens, P.J., Durbin, R., Swerdlow, H. and Turner, D.J. (2008) A large genome center's improvements to the Illumina sequencing system. Nat. Methods, 5, 1005-1010.
2. Li, R., Fan, W., Tian, G., Zhu, H., He, L., Cai, J., Huang, Q., Cai, Q., Li, B., Bai, Y. et al. (2010) The sequence and de novo assembly of the giant panda genome. Nature, 463, 311-317.
3. Fujimoto, A., Nakagawa, H., Hosono, N., Nakano, K., Abe, T., Boroevich, K.A., Nagasaki, M., Yamaguchi, R., Shibuya, T., Kubo, M. et al. (2010) Whole-genome sequencing and comprehensive variant analysis of a Japanese individual using massively parallel sequencing. Nat. Genet., 42, 931-936.
4. Bennett, S. (2004) Solexa Ltd. Pharmacogenomics, 5, 433-438. (Pubitemid 38923657)
5. Margulies, M., Egholm, M., Altman, W.E., Attiya, S., Bader, J.S., Bemben, L.A., Berka, J., Braverman, M.S., Chen, Y.-J., Chen, Z. et al. (2005) Genome sequencing in microfabricated high-density picolitre reactors. Nature, 437, 376-380. (Pubitemid 41613494)
6. Pandey, V., Nutter, R.C. and Prediger, E. (2008) Applied Biosystems SOLiD system: ligation-based sequencing. In Janitz, M. (ed.), Next Generation Genome Sequencing: Toward Personalized Medicine. Wiley, Hoboken, NJ, pp. 29-41.
7. Metzker, M.L. (2010) Sequencing technologies-the next generation. Nat. Rev. Genet., 11, 31-46.
8. Bentley, D.R., Balasubramanian, S., Swerdlow, H.P., Smith, G.P., Milton, J., Brown, C.G., Hall, K.P., Evers, D.J., Barnes, C.L., Bignell, H.R. et al. (2008) Accurate whole human genome sequencing using reversible terminator chemistry. Nature, 456, 53-59.
9. Wang, Z., Gerstein, M. and Snyder, M. (2009) RNA-Seq: a revolutionary tool for transcriptomics. Nat. Rev. Genet., 10, 57-63.
10. Pepke, S., Wold, B. and Mortazavi, A. (2009) Computation for ChIP-seq and RNA-seq studies. Nat. Methods, 6, S22-S32.
11. Zerbino, D.R. and Birney, E. (2008) Velvet: Algorithms for de novo short read assembly using de Bruijn graphs. Genome Res., 18, 821-829. (Pubitemid 351645072)
12. Simpson, J.T., Wong, K., Jackman, S.D., Schein, J.E., Jones, S.J.M. and Birol, I. (2009) ABySS: A parallel assembler for short read sequence data. Genome Res., 19, 1117-1123.
13. Altschul, S.F., Madden, T.L., Schaffer, A.A., Zhang, J., Zhang, Z., Miller, W. and Lipman, D.J. (1997) Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res., 25, 3389-3402. (Pubitemid 27359211)
14. Larkin, M.A., Blackshields, G., Brown, N.P., Chenna, R., McGettigan, P.A., McWilliam, H., Valentin, F., Wallace, I.M., Wilm, A., Lopez, R. et al. (2007) Clustal W and Clustal X version 2.0. Bioinformatics, 23, 2947-2948. (Pubitemid 350162903)
15. Smith, T.F. and Waterman, M.S. (1981) Identification of common molecular subsequences. J. Mol. Biol., 147, 195-197.
16. Needleman, S.B. and Wunsch, C.D. (1970) A general method applicable to the search for similarities in the amino acid sequence of two proteins. J. Mol. Biol., 48, 443-453.
17. Li, H. and Durbin, R. (2010) Fast and accurate long-read alignment with Burrows-Wheeler transform. Bioinformatics, 26, 589-595.
18. Li, H., Ruan, J. and Durbin, R. (2008) Mapping short DNA sequencing reads and calling variants using mapping quality scores. Genome Res., 18, 1851-1858.
19. Kent, W.J. (2002) BLAT-The BLAST-like alignment tool. Genome Res., 12, 656-664.
20. Rumble, S.M., Lacroute, P., Dalca, A.V., Fiume, M., Sidow, A. and Brudno, M. (2009) SHRiMP: Accurate mapping of short color-space reads. PLoS Comput. Biol., 5, e1000386.
21. Li, R., Yu, C., Li, Y., Lam, T.-W., Yiu, S.-M., Kristiansen, K. and Wang, J. (2009) SOAP2: an improved ultrafast tool for short read alignment. Bioinformatics, 25, 1966-1967.
22. Homer, N., Merriman, B. and Nelson, S.F. (2009) BFAST: An alignment tool for large scale genome resequencing. PLoS ONE, 4, e7767.
23. Kozarewa, I., Ning, Z., Quail, M.A., Sanders, M.J., Berriman, M. and Turner, D.J. (2009) Amplification-free Illumina sequencing-library preparation facilitates improved mapping and assembly of (G+C)-biased genomes. Nat. Methods, 6, 291-295.
24. Stein, A., Takasuka, T.E. and Collings, C.K. (2010) Are nucleosome positions in vivo primarily determined by histone-DNA sequence preferences? Nucleic Acids Res., 38, 709-719.
25. Harismendy, O., Ng, P.C., Strausberg, R.L., Wang, X., Stockwell, T.B., Beeson, K.Y., Schork, N.J., Murray, S.S., Topol, E.J., Levy, S. et al. (2009) Evaluation of next generation sequencing platforms for population targeted sequencing studies. Genome Biol., 10, R32.
26. Hoffman, S., Otto, C., Kurtz, S., Sharma, C.M., Khaitovich, P., Vogel, J., Stadler, P.F. and Hackermuller, J. (2009) Fast mapping of short sequences with mismatches, insertions and deletions using index structures. PLoS Comput. Biol., 5, e1000502.
27. Kircher, M., Stenzel, U. and Kelso, J. (2009) Improved base calling for the Illumina Genome Analyzer using machine learning strategies. Genome Biol., 10, R83.
28. Dohm, J.C., Lottaz, C., Borodina, T. and Himmelbauer, H. (2008) Substantial biases in ultra-short read data sets from high-throughput DNA sequencing. Nucleic Acids Res., 36, e105.
29. Milne, I., Bayer, M., Cardle, L., Shaw, P., Stephen, G., Wright, F. and Marshall, D. (2010) Tablet-next generation sequence assmbly visualization. Bioinformatics, 26, 401-402.
30. Cock, P.J.A., Fields, C.J., Goto, N., Heuer, M.L. and Rice, P.M. (2010) The Sanger FASTQ file format for sequences with quality scores, and the Solexa/Illumina FASTQ variants. Nucleic Acids Res., 38, 1767-1771.
31. Rodrigue, S., Materna, A.C., Timberlake, S.C., Blackburn, M.C., Malmstrom, R.R., Alm, E.J. and Chisholm, S.W. (2010) Unlocking short read sequencing for metagenomics. PLoS ONE, 5, e11840.
32. Chaisson, M.J., Brinza, D. and Pevzner, P.A. (2009) De novo fragment assembly with short mate-paired reads: Does the read length matter? Genome Res., 19, 336-346.
33. Farrer, R.A., Kemen, E., Jones, J.D.G. and Studholme, D.J. (2009) De novo assembly of the Pseudomonas syringae pv.syringae B728a genome using Illumina/Solexa short sequence reads. FEMS Microbiol. Lett., 291, 103-111.
34. Tsai, I.J., Otto, T.D. and Berriman, M. (2010) Improving draft assemblies by iterative mapping and assembly of short reads to eliminate gaps. Genome Biol., 11, R41.
35. Medvedev, P., Stanciu, M. and Brudno, M. (2009) Computational methods for discovering structural variation with next-generation sequencing. Nat. Methods, 6, S13-S20.
36. DiGuistini, S., Liao, N.Y., Platt, D., Robertson, G., Seidel, M., Chan, S.K., Docking, T.R., Birol, I., Holt, R.A., Hirst, M. et al. (2009) De novo genome sequence assembly of a filamentous fungus using Sanger, 454 and Illumina sequence data. Genome Biol., 10, R94.
37. Chaisson, M.J. and Pevzner, P.A. (2008) Short read fragment assembly of bacterial genomes. Genome Res., 18, 324-330. (Pubitemid 351240742)
38. Erlich, Y., Mitra, P.P., delaBastide, M., McCombie, W.R. and Hannon, G.J. (2008) Alta-Cyclic: a self-optimizing base caller for next-generation sequencing. Nat. Methods, 5, 679-682.
39. Rougemont, J., Amzallag, A., Iseli, C., Farinelli, L., Xenarios, I. and Naef, F. (2008) Probabilistic base calling of Solexa sequencing data. BMC Bioinformatics, 9, 431-442.