SInC: An accurate and fast error-model based simulator for SNPs, Indels and CNVs coupled with a read generator for short-read sequence data

BMC Bioinformatics

Volumn 15, Issue 1, 2014, Pages

  Pattnaik, Swetansu ^a,b   Gupta, Saurabh ^a   Rao, Arjun A ^a   Panda, Binay ^a,b  

^a Institute of Bioinformatics and Applied Biotechnology   (India)

^b Strand Life Sciences ^*  (India)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; COMPUTER PROGRAM; COMPUTER SIMULATION; DNA SEQUENCE; GENETIC DATABASE; GENETIC POLYMORPHISM; GENETICS; GENOME; GENOMICS; HIGH THROUGHPUT SEQUENCING; INDEL MUTATION; METHODOLOGY;

COMPUTER SIMULATION; DATABASES, GENETIC; GENOME; GENOMICS; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; INDEL MUTATION; POLYMORPHISM, GENETIC; SEQUENCE ANALYSIS, DNA; SOFTWARE;

EID: 84893173383     PISSN: None     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/1471-2105-15-40     Document Type: Article

References (41)

1. Schweiger MR, Kerick M, Timmermann B, Isau M. The power of NGS technologies to delineate the genome organization in cancer: from mutations to structural variations and epigenetic alterations. Canc Metastasis Rev 2011, 30(2):199-210.
2. Shendure J, Ji H. Next-generation DNA sequencing. Nat Biotechnol 2008, 26(10):1135-1145. 10.1038/nbt1486, 18846087.
3. Shendure J, Lieberman Aiden E. The expanding scope of DNA sequencing. Nat Biotechnol 2012, 30(11):1084-1094. 10.1038/nbt.2421, 23138308.
4. McKenna A, Hanna M, Banks E, Sivachenko A, Cibulskis K, Kernytsky A, Garimella K, Altshuler D, Gabriel S, Daly M, et al. The Genome Analysis Toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data. Genome Res 2010, 20(9):1297-1303. 10.1101/gr.107524.110, 2928508, 20644199.
5. Li H. A statistical framework for SNP calling, mutation discovery, association mapping and population genetical parameter estimation from sequencing data. Bioinformatics 2011, 27(21):2987-2993. 10.1093/bioinformatics/btr509, 3198575, 21903627.
6. Ye K, Schulz MH, Long Q, Apweiler R, Ning Z. Pindel: a pattern growth approach to detect break points of large deletions and medium sized insertions from paired-end short reads. Bioinformatics 2009, 25(21):2865-2871. 10.1093/bioinformatics/btp394, 2781750, 19561018.
7. 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.
8. Pattnaik S, Vaidyanathan S, Pooja DG, Deepak S, Panda B. Customisation of the exome data analysis pipeline using a combinatorial approach. PloS One 2012, 7(1):e30080. 10.1371/journal.pone.0030080, 3253117, 22238694.
9. Li H, Durbin R. Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics 2009, 25(14):1754-1760. 10.1093/bioinformatics/btp324, 2705234, 19451168.
10. Homer N, Nelson SF. Improved variant discovery through local re-alignment of short-read next-generation sequencing data using SRMA. Genome Biol 2010, 11(10):R99. 10.1186/gb-2010-11-10-r99, 3218665, 20932289.
11. Lunter G, Goodson M. Stampy: a statistical algorithm for sensitive and fast mapping of Illumina sequence reads. Genome Res 2011, 21(6):936-939. 10.1101/gr.111120.110, 3106326, 20980556.
12. Langmead B. Aligning short sequencing reads with Bowtie. Current protocols in bioinformatics 2010, 32:11.7.1-11.7.14.
13. Liu Y, Schmidt B. Long read alignment based on maximal exact match seeds. Bioinformatics 2012, 28(18):i318-i324. 10.1093/bioinformatics/bts414, 3436841, 22962447.
14. Novoalign Available:http://www.novocraft.com/main/index.php. Accessed 2012 Dec.
15. Ruffalo M, LaFramboise T, Koyuturk M. Comparative analysis of algorithms for next-generation sequencing read alignment. Bioinformatics 2011, 27(20):2790-2796. 10.1093/bioinformatics/btr477, 21856737.
16. Hatem A, Bozdag D, Toland AE, Catalyurek UV. Benchmarking short sequence mapping tools. BMC Bioinforma 2013, 14:184.
17. Krishnan NM, Gaur P, Chaudhary R, Rao AA, Panda B. COPS: a sensitive and accurate tool for detecting somatic Copy Number Alterations using short-read sequence data from paired samples. PloS One 2012, 7(10):e47812. 10.1371/journal.pone.0047812, 3478291, 23110103.
18. Abyzov A, Urban AE, Snyder M, Gerstein M. CNVnator: an approach to discover, genotype, and characterize typical and atypical CNVs from family and population genome sequencing. Genome Res 2011, 21(6):974-984. 10.1101/gr.114876.110, 3106330, 21324876.
19. Xie C, Tammi MT. CNV-seq, a new method to detect copy number variation using high-throughput sequencing. BMC Bioinforma 2009, 10:80.
20. Bentley DR, Balasubramanian S, Swerdlow HP, Smith GP, Milton J, Brown CG, Hall KP, Evers DJ, Barnes CL, Bignell HR, et al. Accurate whole human genome sequencing using reversible terminator chemistry. Nature 2008, 456(7218):53-59. 10.1038/nature07517, 2581791,2581791, 18987734.
21. Ono Y, Asai K, Hamada M. PBSIM: PacBio reads simulator-toward accurate genome assembly. Bioinformatics 2013, 29(1):119-121. 10.1093/bioinformatics/bts649, 23129296.
22. Balzer S, Malde K, Lanzen A, Sharma A, Jonassen I. Characteristics of 454 pyrosequencing data-enabling realistic simulation with flowsim. Bioinformatics 2010, 26(18):i420-i425. 10.1093/bioinformatics/btq365, 2935434, 20823302.
23. Hu X, Yuan J, Shi Y, Lu J, Liu B, Li Z, Chen Y, Mu D, Zhang H, Li N, et al. pIRS: Profile-based Illumina pair-end reads simulator. Bioinformatics 2012, 28(11):1533-1535. 10.1093/bioinformatics/bts187, 22508794.
24. Lysholm F, Andersson B, Persson B. An efficient simulator of 454 data using configurable statistical models. BMC Res Notes 2011, 4(1):449. 10.1186/1756-0500-4-449, 3214204, 22029428.
25. Huang W, Li L, Myers JR, Marth GT. ART: a next-generation sequencing read simulator. Bioinformatics 2012, 28(4):593-594. 10.1093/bioinformatics/btr708, 3278762, 22199392.
26. McElroy KE, Luciani F, Thomas T. GemSIM: general, error-model based simulator of next-generation sequencing data. BMC Genom 2012, 13:74.
27. Holtgrewe M. Mason - a read simulator for second generation sequencing data 2010, Berlin: Freie Universität Berlin.
28. Richter DC, Ott F, Auch AF, Schmid R, Huson DH. MetaSim: a sequencing simulator for genomics and metagenomics. PloS One 2008, 3(10):e3373. 10.1371/journal.pone.0003373, 2556396, 18841204.
29. Engle ML, Burks C. Artificially generated data sets for testing DNA sequence assembly algorithms. Genomics 1993, 16(1):286-288. 10.1006/geno.1993.1180, 8486376.
30. Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, Marth G, Abecasis G, Durbin R. The Sequence Alignment/Map format and SAMtools. Bioinformatics 2009, 25(16):2078-2079. 10.1093/bioinformatics/btp352, 2723002, 19505943.
31. Amigo J, Salas A, Phillips C. ENGINES: exploring single nucleotide variation in entire human genomes. BMC Bioinforma 2011, 12:105.
32. DePristo MA, Banks E, Poplin R, Garimella KV, Maguire JR, Hartl C, Philippakis AA, del Angel G, Rivas MA, Hanna M, et al. A framework for variation discovery and genotyping using next-generation DNA sequencing data. Nat Genet 2011, 43(5):491-498. 10.1038/ng.806, 3083463, 21478889.
33. Mills RE, Pittard WS, Mullaney JM, Farooq U, Creasy TH, Mahurkar AA, Kemeza DM, Strassler DS, Ponting CP, Webber C, et al. Natural genetic variation caused by small insertions and deletions in the human genome. Genome Res 2011, 21(6):830-839. 10.1101/gr.115907.110, 3106316, 21460062.
34. Amigo J, Phillips C, Salas A, Carracedo A. Viability of in-house data mining approaches for population genetics analysis of SNP genotypes. BMC Bioinforma 2009, 10 Suppl 3:S5.
35. Mullaney JM, Mills RE, Pittard WS, Devine SE. Small insertions and deletions (INDELs) in human genomes. Hum Mol Genet 2010, 19(R2):R131-R136. 10.1093/hmg/ddq400, 2953750, 20858594.
36. Redon R, Ishikawa S, Fitch KR, Feuk L, Perry GH, Andrews TD, Fiegler H, Shapero MH, Carson AR, Chen W, et al. Global variation in copy number in the human genome. Nature 2006, 444(7118):444-454. 10.1038/nature05329, 2669898, 17122850.
37. Conrad DF, Pinto D, Redon R, Feuk L, Gokcumen O, Zhang Y, Aerts J, Andrews TD, Barnes C, Campbell P, et al. Origins and functional impact of copy number variation in the human genome. Nature 2010, 464(7289):704-712. 10.1038/nature08516, 3330748, 19812545.
38. Mills RE, Walter K, Stewart C, Handsaker RE, Chen K, Alkan C, Abyzov A, Yoon SC, Ye K, Cheetham RK, et al. Mapping copy number variation by population-scale genome sequencing. Nature 2011, 470(7332):59-65. 10.1038/nature09708, 3077050, 21293372.
39. Park H, Kim JI, Ju YS, Gokcumen O, Mills RE, Kim S, Lee S, Suh D, Hong D, Kang HP, et al. Discovery of common Asian copy number variants using integrated high-resolution array CGH and massively parallel DNA sequencing. Nat Genet 2010, 42(5):400-405. 10.1038/ng.555, 3329635, 20364138.
40. Carter SL, Cibulskis K, Helman E, McKenna A, Shen H, Zack T, Laird PW, Onofrio RC, Winckler W, Weir BA, et al. Absolute quantification of somatic DNA alterations in human cancer. Nature Biotechnology 2012, 30(5):413-421. 10.1038/nbt.2203, 22544022.
41. Ishikawa S, Komura D, Tsuji S, Nishimura K, Yamamoto S, Panda B, Huang J, Fukayama M, Jones KW, Aburatani H. Allelic dosage analysis with genotyping microarrays. Biochem Biophys Res Comm 2005, 333(4):1309-1314. 10.1016/j.bbrc.2005.06.040, 15982637.