PyroHMMsnp: An SNP caller for Ion Torrent and 454 sequencing data

Nucleic Acids Research

Volumn 41, Issue 13, 2013, Pages

  Zeng, Feng ^a   Jiang, Rui ^a   Chen, Ting ^a,b  

^a TSINGHUA UNIVERSITY   (China)

^b UNIVERSITY OF SOUTHERN CALIFORNIA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ACCURACY; ARTICLE; BAYESIAN LEARNING; COMPARATIVE STUDY; DIPLOIDY; ESCHERICHIA COLI; GENOTYPE; HAPLOTYPE; HETEROZYGOSITY; HIDDEN MARKOV MODEL; HOMOZYGOSITY; HUMAN; INFORMATION PROCESSING; INFORMATION RETRIEVAL; NONHUMAN; PREDICTION; PRIORITY JOURNAL; PROBABILITY; PYROSEQUENCING; SENSITIVITY AND SPECIFICITY; SIMULATION; SINGLE NUCLEOTIDE POLYMORPHISM;

ESCHERICHIA COLI; GENOME, BACTERIAL; GENOME, HUMAN; HUMANS; MARKOV CHAINS; POLYMORPHISM, SINGLE NUCLEOTIDE; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS, DNA; SOFTWARE;

EID: 84880533404     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkt372     Document Type: Article

References (45)

1. 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)
2. Rothberg, J.M., Hinz, W., Rearick, T.M., Schultz, J., Mileski, W., Davey, M., Leamon, J.H., Johnson, K., Milgrew, M.J., Edwards, M. et al. (2011) An integrated semiconductor device enabling non-optical genome sequencing. Nature, 475, 348-352.
3. Sims, P.A., Greenleaf, W.J., Duan, H. and Xie, X.S. (2011) Fluorogenic DNA sequencing in PDMS microreactors. Nat. Methods, 8, 575-580.
4. Ronaghi, M., Uhlen, M. and Nyren, P. (1998) A sequencing method based on real-time pyrophosphate. Science, 281, 363-365. (Pubitemid 28340773)
5. Ronaghi, M. (2001) Pyrosequencing sheds light on DNA sequencing. Genome Res., 11, 3-11. (Pubitemid 32117949)
6. Metzker, M.L. (2010) Sequencing technologies - the next generation. Nat. Revi. Genet., 11, 31-46.
7. Turcatti, G., Romieu, A., Fedurco, M. and Tairi, A.P. (2008) A new class of cleavable fluorescent nucleotides: synthesis and optimization as reversible terminators for DNA sequencing by synthesis. Nucleic Acids Res., 36, e25.
8. Shendure, J. and Ji, H. (2008) Next-generation DNA sequencing. Nat. Biotechnol., 26, 1135-1145.
9. Balzer, S., Malde, K., Lanzen, A., Sharma, A. and Jonassen, I. (2010) Characteristics of 454 pyrosequencing data-enabling realistic simulation with flowsim. Bioinformatics, 26, i420-i425.
10. Huse, S.M., Huber, J.A., Morrison, H.G., Sogin, M.L. and Welch, D.M. (2007) Accuracy and quality of massively parallel DNA pyrosequencing. Genome Biol., 8, R143.
11. Wheeler, D.A. (2008) The complete genome of an individual by massively parallel DNA sequencing. Nature, 452, 872-876. (Pubitemid 351550870)
12. Brockman, W., Alvarez, P., Young, S., Garber, M., Giannoukos, G., Lee, W.L., Russ, C., Lander, E.S., Nusbaum, C. and Jaffe, D.B. (2008) Quality scores and SNP detection in sequencing-by-synthesis systems. Genome Res., 18, 763-770. (Pubitemid 351645066)
13. Quinlan, A.R., Stewart, D.A., Stromberg, M.P. and Marth, G.T. (2008) Pyrobayes: an improved base caller for SNP discovery in pyrosequences. Nat. Methods, 5, 179-181. (Pubitemid 351181747)
14. Shen, Y., Wan, Z., Coarfa, C., Drabek, R., Chen, L., Ostrowski, E.A., Liu, Y., Weinstock, G.M., Wheeler, D.A., Gibbs, R.A. et al. (2010) A SNP discovery method to assess variant allele probability from next-generation resequencing data. Genome Res., 20, 273-280.
15. Hoberman, R., Dias, J., Ge, B., Harmsen, E., Mayhew, M., Verlaan, D.J., Kwan, T., Dewar, K., Blanchette, M. and Pastinen, T. (2009) A probabilistic approach for SNP discovery in high-throughput human resequencing data. Genome Res., 19, 1542-1552.
16. Marth, G.T., Korf, I., Yandell, M.D., Yeh, R.T., Gu, Z., Zakeri, H., Stitziel, N.O., Hillier, L., Kwok, P.Y. and Gish, W.R. (1999) A general approach to single-nucleotide polymorphism discovery. Nat. Genet., 23, 452-456.
17. Li, H. (2011) Improving SNP discovery by base alignment quality. Bioinformatics, 27, 1157-1158.
18. DePristo, M.A., Banks, E., Poplin, R., Garimella, K.V., Maguire, J.R., Hartl, C., Philippakis, A.A., del Angel, G., Rivas, M.A., Hanna, M. et al. (2011) A framework for variation discovery and genotyping using next-generation DNA sequencing data. Nat. Genet., 43, 491-498.
19. Albers, C.A., Lunter, G., MacArthur, D.G., McVean, G., Ouwehand, W.H. and Durbin, R. (2011) Dindel: accurate indel calls from short-read data. Genome Res., 21, 961-973.
20. Souaiaia, T., Frazier, Z. and Chen, T. (2011) ComB: SNP calling and mapping analysis for color and nucleotide space platforms. J. Comput. Biol., 18, 795-807.
21. Kofler, R., Teixeira Torres, T., Lelley, T. and Schlotterer, C. (2009) PanGEA: Identification of allele specific gene expression using the 454 technology. BMC Bioinformatics, 10, 143.
22. Lysholm, F. (2012) Highly improved homopolymer aware nucleotide-protein alignments with 454 data. BMC Bioinformatics, 13, 230.
23. Churchill, G.A. and Waterman, M.S. (1992) The accuracy of DNA sequences: estimating sequence quality. Genomics, 14, 89-98.
24. Li, H., Handsaker, B., Wysoker, A., Fennell, T., Ruan, J., Homer, N., Marth, G., Abecasis, G. and Durbin, R. (2009) The Sequence Alignment/Map format and SAMtools. Bioinformatics, 25, 2078-2079.
25. Vacic, V., Jin, H., Zhu, J.K. and Lonardi, S. (2008) A probabilistic method for small RNA flowgram matching. Pac. Symp. Biocomput., 75-86.
26. Zhang, Z., Schwartz, S., Wagner, L. and Miller, W. (2000) A greedy algorithm for aligning DNA sequences. J. Comput. Biol., 7, 203-214. (Pubitemid 30412170)
27. Ning, Z., Cox, A.J. and Mullikin, J.C. (2001) SSAHA: a fast search method for large DNA databases. Genome Res., 11, 1725-1729. (Pubitemid 33040499)
28. Li, H. and Durbin, R. (2010) Fast and accurate long-read alignment with Burrows-Wheeler transform. Bioinformatics, 26, 589-595.
29. Durbin, R., Eddy, S., Krogh, A. and Mitchison, G. (1999) Biological Sequence Analysis: Probabilistic Models of Proteins and Nucleic Acids. Cambridge University Press, Cambridge.
30. Dempster, A.P., Laird, N.M. and Rubin, D.B. (1977) Maximum Likelihood from Incomplete Data via the EM Algorithm. J. R. Stat. Soc. Ser. B, 39, 1-38.
31. Julicher, F. and Bruinsma, R. (1998) Motion of RNA polymerase along DNA: a stochastic model. Biophys. J., 74, 1169-1185. (Pubitemid 28108529)
32. Tadigotla, V.R., Maoileidigh, D.O., Sengupta, A.M., Epshtein, V., Ebright, R.H., Nudler, E. and Ruckenstein, A.E. (2006) Thermodynamic and kinetic modeling of transcriptional pausing. Proc. Natl Acad. Sci. USA, 103, 4439-4444.
33. Elahi, E. and Ronaghi, M. (2004) Pyrosequencing: a tool for DNA sequencing analysis. Methods Mol. Biol., 255, 211-219.
34. Steen, J.A. and Cooper, M.A. (2011) Fluorogenic pyrosequencing in microreactors. Nat. Methods, 8, 548-549.
35. Huang, W., Li, L., Myers, J.R. and Marth, G.T. (2012) ART: a next-generation sequencing read simulator. Bioinformatics, 28, 593-594.
36. Li, S., Li, R., Li, H., Lu, J., Li, Y., Bolund, L., Schierup, M.H. and Wang, J. (2013) SOAPindel: Efficient identification of indels from short paired reads. Genome Res., 23, 195-200.
37. Iqbal, Z., Caccamo, M., Turner, I., Flicek, P. and McVean, G. (2012) De novo assembly and genotyping of variants using colored de Bruijn graphs. Nat. Genet., 44, 226-232.
38. Zeng, F., Jiang, R. and Chen, T. (2013), pyroHMMvar: a sensitive and accurate method to call short INDELS and SNPs for Ion Torrent and 454 data. Submitted.
39. Lee, C., Grasso, C. and Sharlow, M.F. (2002) Multiple sequence alignment using partial order graphs. Bioinformatics, 18, 452-464. (Pubitemid 34284947)
40. Homer, N. and Nelson, S. (2010) Improved variant discovery through local re-alignment of short-read next-generation sequencing data using SRMA. Genome Biol., 11, R99.
41. Li, H. (2012) Exploring single-sample SNP and INDEL calling with whole-genome de novo assembly. Bioinformatics, 28, 1838-1844.
42. Abecasis, G.R., Auton, A., Brooks, L.D., DePristo, M.A., Durbin, R.M., Handsaker, R.E., Kang, H.M., Marth, G.T. and McVean, G.A. (2012) An integrated map of genetic variation from 1,092 human genomes. Nature, 491, 56-65.
43. Le, S.Q. and Durbin, R. (2011) SNP detection and genotyping from low-coverage sequencing data on multiple diploid samples. Genome Res., 21, 952-960.
44. Bansal, V., Harismendy, O., Tewhey, R., Murray, S.S., Schork, N.J., Topol, E.J. and Frazer, K.A. (2010) Accurate detection and genotyping of SNPs utilizing population sequencing data. Genome Res., 20, 537-545.
45. Garrison, E. and Marth, G. (2012) Haplotype-based variant detection from short-read sequencing. eprint, arXiv:1207.3907v2.