Improved base-calling and quality scores for 454 sequencing based on a Hurdle Poisson model

BMC Bioinformatics

Volumn 13, Issue 1, 2012, Pages

  Beuf, Kristof D ^a   Schrijver, Joachim D ^a   Thas, Olivier ^a,b   Criekinge, Wim V ^a   Irizarry, Rafael A ^c   Clement, Lieven ^a,d  

^a GHENT UNIVERSITY   (Belgium)

^b UNIVERSITY OF WOLLONGONG   (Australia)

^c JOHNS HOPKINS BLOOMBERG SCHOOL OF PUBLIC HEALTH   (United States)

^d UNIVERSITY OF LEUVEN   (Belgium)

Author keywords

[No Author keywords available]

Indexed keywords

454-PYROSEQUENCING; APPLICATION FIELDS; DELETION ERRORS; EPIGENETICS; ESCHERICHIA COLI K-12; INSERTION AND DELETION ERRORS; MASSIVELY PARALLELS; METAGENOMICS; NOISE PREDICTORS; POISSON MODEL; PROBABILISTIC FRAMEWORK; REFERENCE DATA; TRANSCRIPTOMICS; USEFUL QUALITIES;

DNA SEQUENCES; ERRORS; ESCHERICHIA COLI; HOMOPOLYMERIZATION;

QUALITY CONTROL;

ESCHERICHIA COLI K12;

ARTICLE; DNA SEQUENCE; ESCHERICHIA COLI K 12; GENE DELETION; GENETICS; POISSON DISTRIBUTION; STATISTICS;

ESCHERICHIA COLI K12; POISSON DISTRIBUTION; SEQUENCE ANALYSIS, DNA; SEQUENCE DELETION;

MLCS; MLOWN;

EID: 84868687174     PISSN: None     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/1471-2105-13-303     Document Type: Article

References (23)

1. Corrada Bravo H, Irizarry RA. Model-based quality assessment and base-calling for second-generation sequencing data. Biometrics 2010, 66:665-674. 10.1111/j.1541-0420.2009.01353.x, 2888717, 19912177.
2. Pop M. Genome assembly reborn: recent computational challenges. Briefings Bioinf 2009, 10(4):354-366.
3. Li H, Ruan J, Durbin R. Mapping short DNA sequencing reads and calling variants using mapping quality scores. Genome Res 2008, 18(11):1851-1858. 10.1101/gr.078212.108, 2577856, 18714091.
4. Quinlan AR, Stewart DA, Stromberg MP, Marth GT. Pyrobayes: an improved base caller for SNP discovery in pyrosequences. Nat Methods 2008, 5(2):179-181. 10.1038/nmeth.1172, 18193056.
5. Hoffmann C, Minkah N, Leipzig J, Wang G, Arens MQ, Tebas P, Bushman FD. DNA bar coding and pyrosequencing to identify rare HIV drug resistance mutations. Nucleic Acids Res 2007, 35(13):e91. 10.1093/nar/gkm435, 1934997, 17576693.
6. Kan Z, Jaiswal BS, Stinson J, Janakiraman V, Bhatt D, Stern HM, Yue P, Haverty PM, Bourgon R, Zheng J, Moorhead M, Chaudhuri S, Tomsho LP, Peters BA, Pujara K, Cordes S, Davis DP, Carlton VEH, Yuan W, Li L, Wang W, Eigenbrot C, Kaminker JS, Eberhard DA, Waring P, Schuster SC, Modrusan Z, Zhang Z, Stokoe D, de Sauvage FJ, Faham M, Seshagiri S. Diverse somatic mutation patterns and pathway alterations in human cancers. Nature 2010, 466(7308):869-873. 10.1038/nature09208, 20668451.
7. Petrosino JF, Highlander S, Luna RA, Gibbs RA, Versalovic J. Metagenomic pyrosequencing and microbial identification. Clin Chem 2009, 55(5):856-866. 10.1373/clinchem.2008.107565, 2892905, 19264858.
8. Margulies M, Egholm M, Altman WE, Attiya S, Bader JS, Bemben LA, Berka J, Braverman MS, Chen YJ, Chen Z, Dewell SB, Du L, Fierro JM, Gomes XV, Godwin BC, He W, Helgesen S, Ho CH, Irzyk GP, Jando SC, Alenquer MLI, Jarvie TP, Jirage KB, Kim JB, Knight JR, Lanza JR, Leamon JH, Lefkowitz SM, Lei M, Li J, et al. Genome sequencing in microfabricated high-density picolitre reactors. Nature 2005, 437(7057):376-380. 1464427, 16056220.
9. Huse S, Huber J, Morrison H, Sogin M, Welch D. Accuracy and quality of massively parallel DNA pyrosequencing. Genome Biol 2007, 8(7):R143. 10.1186/gb-2007-8-7-r143, 2323236, 17659080.
10. Shendure J, Ji H. Next-generation DNA sequencing. Nat Biotech 2008, 26(10):1135-1145.
11. Brockman W, Alvarez P, Young S, Garber M, Giannoukos G, Lee WL, Russ C, Lander ES, Nusbaum C, Jaffe DB. Quality scores and SNP detection in sequencing-by-synthesis systems. Genome Res 2008, 18(5):763-770. 10.1101/gr.070227.107, 2336812, 18212088.
12. Ewing B, Green P. Base-calling of automated sequencer traces using Phred. II. error probabilities. Genome Res 1998, 8(3):186-194.
13. Frith MC, Wan R, Horton P. Incorporating sequence quality data into alignment improves DNA read mapping. Nucleic Acids Res 2010, 38(7):e100. 10.1093/nar/gkq010, 2853142, 20110255.
14. Hamada M, Wijaya E, Frith MC, Asai K. Probabilistic alignments with quality scores: an application to short-read mapping toward accurate SNP/indel detection. Bioinformatics 2011, 27(22):3085-3092. 10.1093/bioinformatics/btr537, 21976422.
15. Albers CA, Lunter G, MacArthur DG, McVean G, Ouwehand WH, Durbin R. Dindel: Accurate indel calls from short-read data. Genome Res 2011, 21(6):961-973. 10.1101/gr.112326.110, 3106329, 20980555.
16. Mullahy J. Specification and testing of some modified count data models. J Econometrics 1986, 33(3):341-365.
17. Ridout MS, Besbeas P. An empirical model for underdispersed count data. Stat Modell 2004, 4:77-89.
18. Hastie TJ, Tibshirani RJ. Generalized additive models 1990, London: Chapman & Hall.
19. McCullagh P, Nelder JA. Generalized Linear Models, Second Edition (Monographs on Statistics and Applied Probability) 1989, London: Chapman & Hall/CRC.
20. Yee T. The VGAM package. R News 2008, 8:28-39.
21. Ning Z, Cox AJ, Mullikin JC. SSAHA: a fast search method for large DNA databases. Genome Res 2001, 11(10):1725-1729. 10.1101/gr.194201, 311141, 11591649.
22. Liao Y, Shi W. Subread: a superfast read aligner with high sensitivity and accuracy (In preparation).
23. Ning Z, Caccamo M, Mullikin JC. ssahaSNP - a polymorphism detection tool on a whole genome scale. 2005 IEEE Comput Syst Bioinf Conference - Workshops 2005, 0:251-252.