ReCoil - an algorithm for compression of extremely large datasets of DNA data

Algorithms for Molecular Biology

Volumn 6, Issue 1, 2011, Pages

  Yanovsky, Vladimir ^a  

^a UNIVERSITY OF TORONTO   (Canada)

Author keywords

[No Author keywords available]

Indexed keywords

EID: 80053647283     PISSN: None     EISSN: 17487188     Source Type: Journal    
DOI: 10.1186/1748-7188-6-23     Document Type: Article

References (18)

1. Chen X, Li M, Ma B, Tromp J. DNACompress: fast and effective DNA sequence compression. Bioinformatics 2002, 18(12):1696-1698. 10.1093/bioinformatics/18.12.1696, 12490460.
2. Ma B, Tromp J, Li M. PatternHunter: faster and more sensitive homology search. Bioinformatics 2002, 18(3):440-445. 10.1093/bioinformatics/18.3.440, 11934743.
3. Timothy White W, Hendy M. Compressing DNA sequence databases with coil. BMC Bioinformatics 2008, 9(1):242. 10.1186/1471-2105-9-242, 2426707, 18489794.
4. Mäkinen V, Navarro G, Sirén J, Välimäki N. Storage and retrieval of individual genomes. Recomb 2009, 121-137.
5. Ferragina P, González R, Navarro G, Venturini R. Compressed Text Indexes: From Theory to Practice. ACM Journal of Experimental Algorithmics (JEA) 2009, 30. 13:article 12.
6. Christley S, Lu Y, Li C, Xie X. Human genomes as email attachments. Bioinformatics 2009, 25(2):274-275. 10.1093/bioinformatics/btn582, 18996942.
7. Kozanitis C, Saunders C, Kruglyak S, Bafna V, Varghese G. Compressing genomic sequence fragments using SlimGene. RECOMB 2010, 310-324.
8. Fritz Hsi-Yang M, Leinonen R, Cochrane G, Birney E. Efficient storage of high throughput DNA sequencing data using reference-based compression. Genome Research 2011, 21(5):734-740. 10.1101/gr.114819.110, 3083090, 21245279.
9. Zhang W, Chen J, Yang Y, Tang Y, Shang J, Shen B. A practical comparison of de novo genome assembly software tools for next-generation sequencing technologies. PLoS ONE 2011, 6(3):e17915.. 3056720, 21423806.
10. Aggarwal A, Vitter S, Jeffrey. The input/output complexity of sorting and related problems. Commun ACM 1988, 31:1116-1127.
11. Dementiev R, Sanders P, Schultes D, Sibeyn JF. Engineering an external memory minimum spanning tree algorithm. IFIP TCS 2004, 195-208.
12. Sommer DD, Delcher AL, Salzberg SL, Pop M. Minimus: a fast, lightweight genome assembler. BMC Bioinformatics 2007, 8:64. 10.1186/1471-2105-8-64, 1821043, 17324286.
13. Buchsbaum AL, Goldwasser M, Venkatasubramanian S, Westbrook JR. On external memory graph traversal. SODA '00: Proceedings of the eleventh annual ACM-SIAM symposium on Discrete algorithms 2000, 859-860. Philadelphia, PA, USA, Society for Industrial and Applied Mathematics, 3213092, 22005130.
14. Ning Z, Cox AJ, Mullikin JC. SSAHA: a fast search method for large dna databases. Genome Research 2001, 11(10):1725-9. 10.1101/gr.194201, 311141, 11591649.
15. Eppstein D, Galil Z, Giancarlo R, Italiano GF. Sparse dynamic programming I: linear cost functions. J ACM 1992, 39(3):519-545.
16. Waterman M, Smith T. Identification of common molecular subsequences. Journal of molecular biology 1981, 147:195-197. 10.1016/0022-2836(81)90087-5, 7265238.
17. Dementiev R, Kettner L. Stxxl: Standard template library for XXL data sets. Proc of ESA 2005 Volume 3669 of LNCS 2005, 640-651. Springer.
18. Ferragina P, Gagie T, Manzini G. Lightweight data indexing and compression in external memory. CoRR, abs/0909.4341 2009,