PERGA: A paired-end read guided de novo assembler for extending contigs using SVM and look ahead approach

PLoS ONE

Volumn 9, Issue 12, 2014, Pages

  Zhu, Xiao ^a   Leung, Henry C M ^b   Chin, Francis Y L ^b   Yiu, Siu Ming ^b   Quan, Guangri ^a   Liu, Bo ^a   Wang, Yadong ^a  

^a HARBIN INSTITUTE OF TECHNOLOGY   (China)

^b UNIVERSITY OF HONG KONG   (Hong Kong)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; BACTERIAL GENOME; GENE DOSAGE; GENE SEQUENCE; GENE STRUCTURE; GENETIC ALGORITHM; HIGH THROUGHPUT SEQUENCING; HUMAN; HUMAN CHROMOSOME; INFORMATION PROCESSING; LOOK AHEAD APPROACH; NONHUMAN; NUCLEOTIDE SEQUENCE; PREDICTION; SUPPORT VECTOR MACHINE; TANDEM REPEAT;

MICROSATELLITE DNA;

HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; MICROSATELLITE REPEATS; SUPPORT VECTOR MACHINE;

EID: 84914703912     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0114253     Document Type: Article

References (33)

1. Shendure J, Porreca GJ, Reppas NB, Lin XX, McCutcheon JP, et al. (2005) Accurate multiplex polony sequencing of an evolved bacterial genome. Science 309: 1728-1732.
2. Margulies M, Egholm M, Altman WE, Attiya S, Bader JS, et al. (2005) Genome sequencing in microfabricated high-density picolitre reactors. Nature 437: 376-380.
3. Li RQ, Fan W, Tian G, Zhu HM, He L, et al. (2010) The sequence and de novo assembly of the giant panda genome. Nature 463: 311-317.
4. Bentley DR, Balasubramanian S, Swerdlow HP, Smith GP, Milton J, et al. (2008) Accurate whole human genome sequencing using reversible terminator chemistry. Nature 456: 53-59.
5. Li H (2012) Exploring single-sample SNP and INDEL calling with whole-genome de novo assembly. Bioinformatics 28: 1838-1844.
6. Blanca JM, Pascual L, Ziarsolo P, Nuez F, Canizares J (2011) ngs-backbone: a pipeline for read cleaning, mapping and SNP calling using Next Generation Sequence. BMC Genomics 12: 285.
7. Schatz MC, Delcher AL, Salzberg SL (2010) Assembly of large genomes using second-generation sequencing. Genome Res 20: 1165-1173.
8. Surget-Groba Y, Montoya-Burgos JI (2010) Optimization of de novo transcriptome assembly from next-generation sequencing data. Genome Res 20: 1432-1440.
9. Treangen TJ, Salzberg SL (2012) Repetitive DNA and next-generation sequencing: computational challenges and solutions. Nat Rev Genet 13: 36-46.
10. Flicek P, Birney E (2009) Sense from sequence reads: methods for alignment and assembly. Nat Methods 6: S6-S12.
11. Shendure J, Ji H (2008) Next-generation DNA sequencing. Nat Biotechnol 26: 1135-1145.
12. Warren RL, Sutton GG, Jones SJ, Holt RA (2007) Assembling millions of short DNA sequences using SSAKE. Bioinformatics 23: 500-501.
13. Jeck WR, Reinhardt JA, Baltrus DA, Hickenbotham MT, Magrini V, et al. (2007) Extending assembly of short DNA sequences to handle error. Bioinformatics 23: 2942-2944.
14. Dohm JC, Lottaz C, Borodina T, Himmelbauer H (2007) SHARCGS, a fast and highly accurate short-read assembly algorithm for de novo genomic sequencing. Genome Res 17: 1697-1706.
15. Hernandez D, Francois P, Farinelli L, Osteras M, Schrenzel J (2008) De novo bacterial genome sequencing: millions of very short reads assembled on a desktop computer. Genome Res 18: 802-809.
16. Miller JR, Delcher AL, Koren S, Venter E, Walenz BP, et al. (2008) Aggressive assembly of pyrosequencing reads with mates. Bioinformatics 24: 2818-2824.
17. Burrows M, Wheeler DJ (1994) A block-sorting lossless data compression algorithm. Technical Report 124: Palo Alto, CA, Digital Equipment Corporation.
18. Simpson JT, Durbin R (2012) Efficient de novo assembly of large genomes using compressed data structures. Genome Res 22: 549-556.
19. Ferragina P, Manzini G (2000) Opportunistic Data Structures with Applications; 2000. pp. IEEE Computer Society, 390-398.
20. Myers EW, Sutton GG, Delcher AL, Dew IM, Fasulo DP, et al. (2000) A whole-genome assembly of Drosophila. Science 287: 2196-2204.
21. Zimin AV, Marcais G, Puiu D, Roberts M, Salzberg SL, et al. (2013) The MaSuRCA genome assembler. Bioinformatics 29: 2669-2677.
22. Pevzner PA, Tang H, Waterman MS (2001) An Eulerian path approach to DNA fragment assembly. Proc Natl Acad Sci USA 98: 9748-9753.
23. Zerbino DR, Birney E (2008) Velvet: algorithms for de novo short read assembly using de Bruijn graphs. Genome Res 18: 821-829.
24. Chaisson MJ, Pevzner PA (2008) Short read fragment assembly of bacterial genomes. Genome Res 18: 324-330.
25. Butler J, MacCallum I, Kleber M, Shlyakhter IA, Belmonte MK, et al. (2008) ALLPATHS: de novo assembly of whole-genome shotgun microreads. Genome Res 18: 810-820.
26. Simpson JT, Wong K, Jackman SD, Schein JE, Jones SJ, et al. (2009) ABySS: A parallel assembler for short read sequence data. Genome Res 19: 1117-1123.
27. Peng Y, Leung HCM, Yiu SM, Chin FYL (2010) IDBA - A Practical Iterative de Bruijn Graph De Novo Assembler. Research in Computational Molecular Biology, Proceedings 6044: 426-440.
28. Peng Y, Leung HC, Yiu SM, Chin FY (2012) IDBA-UD: a de novo assembler for single-cell and metagenomic sequencing data with highly uneven depth. Bioinformatics 28: 1420-1428.
29. Li R, Zhu H, Ruan J, Qian W, Fang X, et al. (2009) De novo assembly of human genomes with massively parallel short read sequencing. Genome Res 20: 265-272.
30. McElroy KE, Luciani F, Thomas T (2012) GemSIM: general, error-model based simulator of next-generation sequencing data. BMC Genomics 13: 74.
31. Kelley DR, Schatz MC, Salzberg SL (2010) Quake: quality-aware detection and correction of sequencing errors. Genome Biol 11: R116.
32. Salzberg SL, Phillippy AM, Zimin A, Puiu D, Magoc T, et al. (2012) GAGE: A critical evaluation of genome assemblies and assembly algorithms. Genome Res 22: 557-567.
33. Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ (1990) Basic local alignment search tool. J Mol Biol 215: 403-410.