Probabilistic model based error correction in a set of various mutant sequences analyzed by next-generation sequencing

Computational Biology and Chemistry

Volumn 47, Issue , 2013, Pages 221-230

  Aita, Takuyo ^a   Ichihashi, Norikazu ^a,b   Yomo, Tetsuya ^a,b  

^a JAPAN SCIENCE AND TECHNOLOGY AGENCY   (Japan)

^b OSAKA UNIVERSITY   (Japan)

Author keywords

Base call error; Image restoration; Quality score; Quasispecies; Sequence analysis; SMRT

Indexed keywords

IMAGE RECONSTRUCTION; PROBABILITY DISTRIBUTIONS; QUALITY CONTROL;

HETEROGENEOUS POPULATIONS; INFORMATION ENGINEERINGS; MAXIMUM A POSTERIORI PROBABILITIES; NEXT-GENERATION SEQUENCING; PROBABILISTIC MODELING; QUASISPECIES; SEQUENCE ANALYSIS; SMRT;

ERROR CORRECTION;

DNA;

ALGORITHM; ARTICLE; BASE CALL ERROR; DNA SEQUENCE; GENETIC VARIABILITY; GENETICS; HIGH THROUGHPUT SEQUENCING; IMAGE RECONSTRUCTION; MUTATION; QUALITY SCORE; QUASISPECIES; SEQUENCE ANALYSIS; SMRT; STATISTICAL MODEL;

BASE CALL ERROR; IMAGE RESTORATION; QUALITY SCORE; QUASISPECIES; SEQUENCE ANALYSIS; SMRT;

ALGORITHMS; DNA; GENETIC VARIATION; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; MODELS, STATISTICAL; MUTATION; SEQUENCE ANALYSIS, DNA;

EID: 84887274212     PISSN: 14769271     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.compbiolchem.2013.09.006     Document Type: Article

References (33)

1. I. Astrovskaya, B. Tork, S. Mangul, K. Westbrooks, I. Mndoiu, P. Balfe, and A. Zelikovsky Inferring viral quasispecies spectra from 454 pyrosequencing reads BMC Bioinformatics 2011 12(Suppl 6): S1
2. J.E. Barrick, D.S. Yu, S.H. Yoon, H. Jeong, T.K. Oh, D. Schneider, R.E. Lenski, and J.F. Kim Genome evolution and adaptation in a long-term experiment with Escherichia coli Nature 461 2009 1243 1247
3. A.J. Betancourt Genomewide patterns of substitution in adaptively evolving populations of the RNA bacteriophage MS2 Genetics 181 2009 1535 1544
4. G.L. Bilbro, W.E. Snyder, S.J. Garnier, and J.W. Gault Mean field annealing: a formalism for constructing GNC-like algorithms IEEE Transactions on Neural Networks 3 1992 131 138
5. P.J. Cock, C.J. Fields, N. Goto, M.L. Heuer, and P.M. Rice The Sanger FASTQ file format for sequences with quality scores and the Solexa/Illumina FASTQ variants Nucleic Acids Research 38 2010 1767 1771
6. J. Eid, A. Fehr, J. Gray, K. Luong, J. Lyle, G. Otto, P. Peluso, D. Rank, P. Baybayan, B. Bettman, A. Bibillo, K. Bjornson, B. Chaudhuri, F. Christians, R. Cicero, S. Clark, R. Dalal, A. Dewinter, J. Dixon, M. Foquet, A. Gaertner, P. Hardenbol, C. Heiner, K. Hester, D. Holden, G. Kearns, X. Kong, R. Kuse, Y. Lacroix, S. Lin, P. Lundquist, C. Ma, P. Marks, M. Maxham, D. Murphy, I. Park, T. Pham, M. Phillips, J. Roy, R. Sebra, G. Shen, J. Sorenson, A. Tomaney, K. Travers, M. Trulson, J. Vieceli, J. Wegener, D. Wu, A. Yang, D. Zaccarin, P. Zhao, F. Zhong, J. Korlach, and S. Turner Real-time DNA sequencing from single polymerase molecules Science 323 2009 133 138
7. M. Eigen, and R. Winkler-Oswatitsch Statistical geometry on sequence space Methods in Enzymology 183 1990 505 530 (Pubitemid 20148839)
8. J.C. Gower Metric and Euclidean properties of dissimilarity coefficients Journal of Classification 3 1986 5 48
9. N. Ichihashi, K. Usui, Y. Kazuta, T. Sunami, T. Matsuura, and T. Yomo Darwinian evolution in a translation-coupled RNA replication system within a cell-like compartment Nature Communications 4 2013 2494 doi:10.1038/ncomms3494
10. L. Ilie, F. Fazayeli, and S. Ilie HiTEC: accurate error correction in high-throughput sequencing data Bioinformatics 27 2011 295 302
11. H. Kita, T. Matsuura, T. Sunami, K. Hosoda, N. Ichihashi, K. Tsukada, I. Urabe, and T. Yomo Replication of genetic information with self-encoded replicase in liposomes ChemBiochem 9 2008 2403 2410
12. L. Liu, Y. Li, S. Li, N. Hu, Y. He, R. Pong, D. Lin, L. Lu, and M. Law Comparison of next-generation sequencing systems Journal of Biomedicine and Biotechnology 2012 251364
13. A.R. Macalalad, M.C. Zody, P. Charlebois, N.J. Lennon, R.M. Newman, C.M. Malboeuf, E.M. Ryan, C.L. Boutwell, K.A. Power, D.E. Brackney, K.N. Pesko, J.Z. Levin, G.D. Ebel, T.M. Allen, B.W. Birren, and M.R. Henn Highly sensitive and specific detection of rare variants in mixed viral populations from massively parallel sequence data PLOS Computational Biology 8 2012 e1002417
14. K. McElroy, O. Zagordi, R. Bull, F. Luciani, and N. Beerenwinkel Accurate single nucleotide variant detection in viral populations by combining probabilistic clustering with a statistical test of strand bias BMC Genomics 14 2013 501
15. J.R. Meyer, D.T. Dobias, J.S. Weitz, J.E. Barrick, R.T. Quick, and R.E. Lenski Repeatability and contingency in the evolution of a key innovation in phage lambda Science 335 2012 428 432
16. J. Otwinowski, and I. Nemenman Genotype to phenotype mapping and the fitness landscape of the E. coli lac promoter PLoS ONE 8 2013 e61570
17. J.N. Pitt, and A.R. Ferr-D'Amar Rapid construction of empirical RNA fitness landscapes Science 330 2010 376 379
18. M.C. Prosperi, L. Prosperi, A. Bruselles, I. Abbate, G. Rozera, D. Vincenti, M.C. Solmone, M.R. Capobianchi, and G. Ulivi Combinatorial analysis and algorithms for quasispecies reconstruction using next-generation sequencing BMC Bioinformatics 12 2011 5
19. M.C. Prosperi, and M. Salemi QuRe: software for viral quasispecies reconstruction from next-generation sequencing data Bioinformatics 28 2012 132 133
20. J.M. Pryce, and A.D. Bruce Statistical mechanics of image restoration Journal of Physics A 28 1995 511 532
21. M.A. Quail, M. Smith, P. Coupland, T.D. Otto, S.R. Harris, T.R. Connor, A. Bertoni, H.P. Swerdlow, and Y. Gu A tale of three next generation sequencing platforms: comparison of Ion Torrent, Pacific Biosciences and Illumina MiSeq sequencers BMC Genomics 13 2012 341
22. P. Skums, Z. Dimitrova, D.S. Campo, G. Vaughan, L. Rossi, J.C. Forbi, J. Yokosawa, A. Zelikovsky, and Y. Khudyakov Efficient error correction for next-generation sequencing of viral amplicons BMC Bioinformatics 25 2012 13
23. L. Steinbruck, and A.C. McHardy Allele dynamics plots for the study of evolutionary dynamics in viral populations Nucleic Acids Research 39 2011 e4
24. K. Tanaka, and T. Morita Cluster variation method and image restoration problem Physics Letters A 203 1995 122 128
25. K. Tanaka, and J. Inoue Maximum likelihood hyperparameter estimation for solvable Markov random field model in image restoration IEICE Transactions on Information and Systems E84-D 2002 546 557 (Pubitemid 35353992)
26. E. Wijaya, M.C. Frith, Y. Suzuki, and P. Horton Recount: expectation maximization based error correction tool for next generation sequencing data Genome Informatics 23 2009 189 201
27. X. Yang, S. Aluru, and K.S. Dorman Repeat-aware modeling and correction of short read errors BMC Bioinformatics 12 2011 S52
28. X. Yang, S.P. Chockalingam, and S. Aluru A survey of error-correction methods for next-generation sequencing Briefings in Bioinformatics 14 2013 56 66
29. O. Zagordi, R. Klein, M. Dumer, and N. Beerenwinkel Error correction of next-generation sequencing data and reliable estimation of HIV quasispecies Nucleic Acids Research 38 2010 7400 7409
30. O. Zagordi, L. Geyrhofer, V. Roth, and N. Beerenwinkel Deep sequencing of a genetically heterogeneous sample: local haplotype reconstruction and read error correction Journal of Computational Biology 17 2010 417 428
31. O. Zagordi, A. Bhattacharya, N. Eriksson, and N. Beerenwinkel ShoRAH: estimating the genetic diversity of a mixed sample from next-generation sequencing data BMC Bioinformatics 12 2011 119
32. X. Zhao, L.E. Palmer, R. Bolanos, C. Mircean, D. Fasulo, and G.M. Wittenberg EDAR: an efficient error detection and removal algorithm for next generation sequencing data Journal of Computational Biology 17 2010 1549 1560
33. Z. Zhou, R.M. Leahy, and J. Qi Approximate maximum likelihood hyperparameter estimation for Gibbs priors IEEE Transactions on Image Processing 6 1997 844 861 (Pubitemid 127768398)