Quake: Quality-aware detection and correction of sequencing errors

Genome Biology

Volumn 11, Issue 11, 2010, Pages

  Kelley, David R ^a   Schatz, Michael C ^b   Salzberg, Steven L ^a  

^a University of Maryland ^*  (United States)

^b Howard Hughes Medical Institute Cold Spring Harbor Laboratory Cold Spring Harbor   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

NUCLEOTIDE; BACTERIAL DNA;

ACCURACY; ARTICLE; COMPUTER PROGRAM; CONTROLLED STUDY; DNA SEQUENCE; ERROR; MAXIMUM LIKELIHOOD METHOD; NONHUMAN; NUCLEOTIDE SEQUENCE; QUALITY CONTROL; SINGLE NUCLEOTIDE POLYMORPHISM; ALGORITHM; BIOLOGICAL MODEL; BIOLOGY; ESCHERICHIA COLI; GENETICS; HUMAN; HUMAN GENOME; METHODOLOGY; SEQUENCE ALIGNMENT; STATISTICAL MODEL;

ALGORITHMS; COMPUTATIONAL BIOLOGY; DNA, BACTERIAL; ESCHERICHIA COLI; GENOME, HUMAN; HUMANS; LIKELIHOOD FUNCTIONS; MODELS, BIOLOGICAL; POLYMORPHISM, SINGLE NUCLEOTIDE; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS, DNA; SOFTWARE;

EID: 78649358717     PISSN: 14747596     EISSN: 1474760X     Source Type: Journal    
DOI: 10.1186/gb-2010-11-11-r116     Document Type: Article

References (51)

1. Shendure J, Ji H. Next-generation DNA sequencing. Nat Biotechnol 2008, 26:1135-1145. 10.1038/nbt1486, 18846087.
2. Hawkins R, Hon G, Ren B. Next-generation genomics: an integrative approach. Nat Rev Genet 2010, 11:476-486.
3. Siva N. 1000 Genomes project. Nat Biotechnol 2008, 26:256.
4. Haussler D, O'Brien S, Ryder O, Barker F, Clamp M, Crawford A, Hanner R, Hanotte O, Johnson W, McGuire J, Miller W, Murphy R, Murphy W, Sheldon F, Sinervo B, Venkatesh B, Wiley E, Allendorf F, Amato G, Baker C, Bauer A, Beja-Pereira A, Bermingham E, Bernardi G, Bonvicino C, Brenner S, Burke T, Cracraft J, Diekhans M, Edwards S, et al. Genome 10K: a proposal to obtain whole-genome sequence for 10 000 vertebrate species. J Hered 2009, 100:659-674. 10.1093/jhered/esp086, 2877544, 19892720.
5. Mardis E. Cancer genomics identifies determinants of tumor biology. Genome Biol 2010, 11:211. 10.1186/gb-2010-11-5-211, 20441611.
6. Robison K. Application of second-generation sequencing to cancer genomics. Brief Bioinform 2010, 11:524-534. 10.1093/bib/bbq013, 20427421.
7. Palmer L, Dejori M, Bolanos R, Fasulo D. Improving de novo sequence assembly using machine learning and comparative genomics for overlap correction. BMC Bioinformatics 2010, 11:33. 10.1186/1471-2105-11-33, 2824677, 20078885.
8. Trapnell C, Salzberg S. How to map billions of short reads onto genomes. Nat Biotechnol 2009, 27:455-7. 10.1038/nbt0509-455, 2836519, 19430453.
9. Pevzner P, Tang H, Waterman M. An Eulerian path approach to DNA fragment assembly. Proc Natl Acad Sci USA 2001, 98:9748. 10.1073/pnas.171285098, 55524, 11504945.
10. Chaisson M, Brinza D, Pevzner P. De novo fragment assembly with short mate-paired reads: does the read length matter?. Genome Res 2009, 19:336. 10.1101/gr.079053.108, 2652199, 19056694.
11. Butler J, MacCallum I, Kleber M, Shlyakhter IA, Belmonte MK, Lander ES, Nusbaum C, Jaffe DB. ALLPATHS: de novo assembly of whole-genome shotgun microreads. Genome Res 2008, 18:810-820. 10.1101/gr.7337908, 2336810, 18340039.
12. Shi H, Schmidt B, Liu W, Muller-Wittig W. A parallel algorithm for error correction in high-throughput short-read data on CUDA-enabled graphics hardware. J Comput Biol 2010, 17:603-615. 10.1089/cmb.2009.0062, 20426693.
13. Li R, Zhu H, Ruan J, Qian W, Fang X, Shi Z, Li Y, Li S, Shan G, Kristiansen K, Li S, Yang H, Wang J, Wang J. De novo assembly of human genomes with massively parallel short read sequencing. Genome Res 2010, 20:265-272. 10.1101/gr.097261.109, 2813482, 20019144.
14. Yang X, Dorman K, Aluru S. Reptile: representative tiling for short read error correction. Bioinformatics 2010, 26:2526-2533. 10.1093/bioinformatics/btq468, 20834037.
15. Gajer P, Schatz M, Salzberg S. Automated correction of genome sequence errors. Nucleic Acids Res 2004, 32:562. 10.1093/nar/gkh216, 373340, 14744981.
16. Batzoglou S, Jaffe D, Stanley K, Butler J, Gnerre S, Mauceli E, Berger B, Mesirov J, Lander E. ARACHNE: a whole-genome shotgun assembler. Genome Res 2002, 12:177. 10.1101/gr.208902, 155255, 11779843.
17. Tammi MT, Arner E, Kindlund E, Andersson B. Correcting errors in shotgun sequences. Nucleic Acids Res 2003, 31:4663-4672. 10.1093/nar/gkg653;, 169956, 12888528.
18. Schroder J, Schroder H, Puglisi SJ, Sinha R, Schmidt B. SHREC: a short-read error correction method. Bioinformatics 2009, 25:2157-2163. 10.1093/bioinformatics/btp379, 19542152.
19. Salmela L. Correction of sequencing errors in a mixed set of reads. Bioinformatics 2010, 26:1284. 10.1093/bioinformatics/btq151, 20378555.
20. Zerbino D, Birney E. Velvet: algorithms for de novo short read assembly using de Bruijn graphs. Genome Res 2008, 18:821. 10.1101/gr.074492.107, 2336801, 18349386.
21. Simpson J, Wong K, Jackman S, Schein J, Jones S, Birol I. ABySS: a parallel assembler for short read sequence data. Genome Res 2009, 19:1117. 10.1101/gr.089532.108, 2694472, 19251739.
22. Qu W, Hashimoto S, Morishita S. Efficient frequency-based de novo short-read clustering for error trimming in next-generation sequencing. Genome Res 2009, 19:1309-1315. 10.1101/gr.089151.108, 2704438, 19439514.
23. Wijaya E, Frith M, Suzuki Y, Horton P. Recount: expectation maximization based error correction tool for next generation sequencing data. Genome Inform 2009, 23:189-201. full_text, 20180274.
24. Zagordi O, Geyrhofer L, Roth V, Beerenwinkel N. Deep sequencing of a genetically heterogeneous sample: local haplotype reconstruction and read error correction. J Comput Biol 2010, 17:417-428. 10.1089/cmb.2009.0164, 20377454.
25. Quince C, Lanzen A, Curtis T, Davenport R, Hall N, Head I, Read L, Sloan W. Accurate determination of microbial diversity from 454 pyrosequencing data. Nat Methods 2009, 6:639-641. 10.1038/nmeth.1361, 19668203.
26. 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:e105+. 10.1093/nar/gkn425, 2532726, 18660515.
27. Bravo H, Irizarry R. 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.
28. Kao W, Stevens K, Song Y. BayesCall: a model-based base-calling algorithm for high-throughput short-read sequencing. Genome Res 2009, 19:1884. 10.1101/gr.095299.109, 2765266, 19661376.
29. Erlich Y, Mitra P, de la Bastide M, McCombie W, Hannon G. Alta-Cyclic: a self-optimizing base caller for next-generation sequencing. Nat Methods 2008, 5:679. 10.1038/nmeth.1230, 2978646, 18604217.
30. Kircher M, Stenzel U, Kelso J. Improved base calling for the Illumina Genome Analyzer using machine learning strategies. Genome Biol 2009, 10:R83. 10.1186/gb-2009-10-8-r83, 2745764, 19682367.
31. Rougemont J, Amzallag A, Iseli C, Farinelli L, Xenarios I, Naef F. Probabilistic base calling of Solexa sequencing data. BMC Bioinformatics 2008, 9:431. 10.1186/1471-2105-9-431, 2575221, 18851737.
32. Quake. , http://www.cbcb.umd.edu/software/quake
33. Perl Artistic License. , http://www.perl.com/pub/a/language/misc/Artistic.html
34. Li H, Ruan J, Durbin R. Mapping short DNA sequencing reads and calling variants using mapping quality scores. Genome Res 2008, 18:1851. 10.1101/gr.078212.108, 2577856, 18714091.
35. Cordaux R, Batzer M. The impact of retrotransposons on human genome evolution. Nat Rev Genet 2009, 10:691-703. 10.1038/nrg2640, 2884099, 19763152.
36. Myers E. Toward simplifying and accurately formulating fragment assembly. J Comput Biol 1995, 2:275-290. 10.1089/cmb.1995.2.275, 7497129.
37. Kurtz S, Phillippy A, Delcher A, Smoot M, Shumway M, Antonescu C, Salzberg S. Versatile and open software for comparing large genomes. Genome Biol 2004, 5:R12. 10.1186/gb-2004-5-2-r12, 395750, 14759262.
38. Pleasance ED, Cheetham RK, Stephens PJ, McBride DJ, Humphray SJ, Greenman CD, Varela I, Lin MLL, Ordonez GR, Bignell GR, Ye K, Alipaz J, Bauer MJ, Beare D, Butler A, Carter RJ, Chen L, Cox AJ, Edkins S, Kokko-Gonzales PI, Gormley NA, Grocock RJ, Haudenschild CD, Hims MM, James T, Jia M, Kingsbury Z, Leroy C, Marshall J, Menzies A, et al. A comprehensive catalogue of somatic mutations from a human cancer genome. Nature 2010, 463:191-196. 10.1038/nature08658, 20016485.
39. Kendal W. An exponential dispersion model for the distribution of human single nucleotide polymorphisms. Mol Biol Evol 2003, 20:579. 10.1093/molbev/msg057, 12679541.
40. Langmead B, Trapnell C, Pop M, Salzberg S. Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol 2009, 10:R25. 10.1186/gb-2009-10-3-r25, 2690996, 19261174.
41. Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, Marth G, Abecasis G, Durbin R, Subgroup GPDP. The sequence alignment/Map format and SAMtools. Bioinformatics 2009, 25:2078. 10.1093/bioinformatics/btp352, 2723002, 19505943.
42. Ahn SM, Kim TH, Lee S, Kim D, Ghang H, Kim DS, Kim BC, Kim SY, Kim WY, Kim C, Park D, Lee YS, Kim S, Reja R, Jho S, Kim CG, Cha JY, Kim KH, Lee B, Bhak J, Kim SJ. The first Korean genome sequence and analysis: full genome sequencing for a socio-ethnic group. Genome Res 2009, 19:1622-1629. 10.1101/gr.092197.109, 2752128, 19470904.
43. Hadoop. , http://hadoop.apache.org
44. Dagum L, Menon R. Open MP: an industry-standard API for shared-memory programming. IEEE Comput Sci Eng 1998, 5:46-55.
45. Dean J, Ghemawat S. MapReduce: simplified data processing on large clusters. Commun ACM 2008, 51:107-113.
46. Chin F, Leung H, Li W, Yiu S. Finding optimal threshold for correction error reads in DNA assembling. BMC Bioinformatics 2009, 10 Suppl 1:S15. 10.1186/1471-2105-10-S1-S15, 2648749, 19208114.
47. Johnson N, Kemp A, Kotz S. Univariate Discrete Distributions 2005, New York: Wiley-Interscience.
48. R: A Language and Environment for Statistical Computing. , http://www.R-project.org
49. Li M, Nordborg M, Li LM. Adjust quality scores from alignment and improve sequencing accuracy. Nucleic Acids Res 2004, 32:5183-5191. 10.1093/nar/gkh850, 521663, 15459287.
50. Li R, Li Y, Fang X, Yang H, Wang J, Kristiansen K, Wang J. SNP detection for massively parallel whole-genome resequencing. Genome Res 2009, 19:1124. 10.1101/gr.088013.108, 2694485, 19420381.
51. Hastie T, Tibshirani R, Friedman J. The Elements of Statistical Learning 2009, Berlin: Springer.