DIDA: Distributed indexing dispatched alignment

PLoS ONE

Volumn 10, Issue 4, 2015, Pages

  Mohamadi, Hamid ^a,b,d   Vandervalk, Benjamin P ^a   Raymond, Anthony ^a   Jackman, Shaun D ^a,b   Chu, Justin ^a,b   Breshears, Clay P ^d   Birol, Inanc ^a,b,c  

^a BRITISH COLUMBIA CANCER AGENCY   (Canada)

^b UNIVERSITY OF BRITISH COLUMBIA   (Canada)

^c SIMON FRASER UNIVERSITY   (Canada)

^d INTEL CORPORATION   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

AMINO ACID; NUCLEOTIDE;

AMINO ACID SEQUENCE; ARTICLE; BIOINFORMATICS; CAENORHABDITIS ELEGANS; CONTROLLED STUDY; DISTRIBUTED INDEXING DISPATCHED ALIGNMENT; FALSE POSITIVE RESULT; HIGH THROUGHPUT SEQUENCING; NONHUMAN; NUCLEOTIDE SEQUENCE; PROBABILITY; SEQUENCE ALIGNMENT; TASK PERFORMANCE; BIOLOGY; GENETIC DATABASE; HUMAN; PROCEDURES; SOFTWARE;

COMPUTATIONAL BIOLOGY; DATABASES, GENETIC; HUMANS; SEQUENCE ALIGNMENT; SOFTWARE;

EID: 84928795234     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0126409     Document Type: Article

References (42)

1. Meek C, Patel JM, Kasetty S (2003) Oasis: An online and accurate technique for local-alignment searches on biological sequences. In: Proceedings of the 29th International Conference on Very Large Data Bases-Volume 29. VLDB Endowment, VLDB '03, pp. 910-921. http://dl.acm.org/citation.cfm?id=1315451.1315529.
2. Kurtz S, Phillippy A, Delcher A, Smoot M, Shumway M, et al. (2004) Versatile and open software for comparing large genomes. Genome Biology 5: R12. doi: 10.1186/gb-2004-5-2-r12 PMID: 14759262
3. Abouelhoda M, Kurtz S, Ohlebusch E (2002) The enhanced suffix array and its applications to genome analysis. In: Guigó R, Gusfield D, editors, Algorithms in Bioinformatics, Springer Berlin Heidelberg, volume 2452 of Lecture Notes in Computer Science. pp. 449-463. http://dx.doi.org/10.1007/3-540-45784-4-35.
4. Hoffmann S, Otto C, Kurtz S, Sharma CM, Khaitovich P, et al. (2009) Fast mapping of short sequences with mismatches, insertions and deletions using index structures. PLoS Comput Biol 5: e1000502. doi: 10.1371/journal.pcbi.1000502 PMID: 19750212
5. Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ (1990) Basic local alignment search tool. Journal of Molecular Biology 215: 403-410. doi: 10.1016/S0022-2836(05)80360-2 PMID: 2231712
6. Chen Y, Souaiaia T, Chen T (2009) Perm: efficient mapping of short sequencing reads with periodic full sensitive spaced seeds. Bioinformatics 25: 2514-2521. doi: 10.1093/bioinformatics/btp486 PMID: 19675096
7. Hach F, Hormozdiari F, Alkan C, Hormozdiari F, Birol I, et al. (2010) mrsfast: a cache-oblivious algorithm for short-read mapping. Nat Meth 7: 576-577. doi: 10.1038/nmeth0810-576
8. Homer N, Merriman B, Nelson SF (2009) Bfast: An alignment tool for large scale genome resequencing. PLoS ONE 4: e7767. doi: 10.1371/journal.pone.0007767 PMID: 19907642
9. Li H, Ruan J, Durbin R (2008) Mapping short dna sequencing reads and calling variants using mapping quality scores. Genome Research 18: 1851-1858. doi: 10.1101/gr.078212.108 PMID: 18714091
10. Ma B, Tromp J, Li M (2002) Patternhunter: faster and more sensitive homology search. Bioinformatics 18: 440-445. doi: 10.1093/bioinformatics/18.3.440 PMID: 11934743
11. Schatz MC (2009) Cloudburst: highly sensitive read mapping with mapreduce. Bioinformatics 25: 1363-1369. doi: 10.1093/bioinformatics/btp236 PMID: 19357099
12. Smith AD, Chung WY, Hodges E, Kendall J, Hannon G, et al. (2009) Updates to the rmap short-read mapping software. Bioinformatics 25: 2841-2842. doi: 10.1093/bioinformatics/btp533 PMID: 19736251
13. Wu TD, Nacu S (2010) Fast and snp-tolerant detection of complex variants and splicing in short reads. Bioinformatics 26: 873-881. doi: 10.1093/bioinformatics/btq057 PMID: 20147302
14. Lam TW, Sung WK, Tam SL, Wong CK, Yiu SM (2008) Compressed indexing and local alignment of dna. Bioinformatics 24: 791-797. doi: 10.1093/bioinformatics/btn032 PMID: 18227115
15. Langmead B, Salzberg SL (2012) Fast gapped-read alignment with bowtie 2. Nat Meth 9: 357-359. doi: 10.1038/nmeth.1923
16. Langmead B, Trapnell C, Pop M, Salzberg S (2009) Ultrafast and memory-efficient alignment of short dna sequences to the human genome. Genome Biology 10: R25. doi: 10.1186/gb-2009-10-3-r25 PMID: 19261174
17. Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, et al. (2009) The sequence alignment/map format and samtools. Bioinformatics 25: 2078-2079. doi: 10.1093/bioinformatics/btp352 PMID: 19505943
18. Li R, Fan W, Tian G, Zhu H, He L, et al. (2010) The sequence and de novo assembly of the giant panda genome. Nature 463: 311-317. doi: 10.1038/nature08696 PMID: 20010809
19. Li R, Yu C, Li Y, Lam TW, Yiu SM, et al. (2009) Soap2: an improved ultrafast tool for short read alignment. Bioinformatics 25: 1966-1967. doi: 10.1093/bioinformatics/btp336 PMID: 19497933
20. Marco-Sola S, Sammeth M, Guigo R, Ribeca P (2012) The gem mapper: fast, accurate and versatile alignment by filtration. Nat Meth 9: 1185-1188. doi: 10.1038/nmeth.2221
21. Butler J, MacCallum I, Kleber M, Shlyakhter IA, Belmonte MK, et al. (2008) Allpaths: De novo assembly of whole-genome shotgun microreads. Genome Research 18: 810-820. doi: 10.1101/gr.7337908 PMID: 18340039
22. Myers EW (2005) The fragment assembly string graph. Bioinformatics 21: ii79-ii85. doi: 10.1093/bioinformatics/bti1114 PMID: 16204131
23. Simpson JT, Durbin R (2012) Efficient de novo assembly of large genomes using compressed data structures. Genome Research 22: 549-556. doi: 10.1101/gr.126953.111 PMID: 22156294
24. Simpson JT, Wong K, Jackman SD, Schein JE, Jones SJ, et al. (2009) Abyss: A parallel assembler for short read sequence data. Genome Research 19: 1117-1123. doi: 10.1101/gr.089532.108 PMID: 19251739
25. Zerbino DR, Birney E (2008) Velvet: Algorithms for de novo short read assembly using de bruijn graphs. Genome Research 18: 821-829. doi: 10.1101/gr.074492.107 PMID: 18349386
26. Birol I, Raymond A, Jackman SD, Pleasance S, Coope R, et al. (2013) Assembling the 20 gb white spruce (picea glauca) genome from whole-genome shotgun sequencing data. Bioinformatics 29: 1492-1497. doi: 10.1093/bioinformatics/btt178 PMID: 23698863
27. Bloom BH (1970) Space/time trade-offs in hash coding with allowable errors. Commun ACM 13: 422-426. doi: 10.1145/362686.362692
28. Chikhi R, Rizk G (2013) Space-efficient and exact de bruijn graph representation based on a bloom filter. Algorithms for Molecular Biology 8: 22. doi: 10.1186/1748-7188-8-22 PMID: 24040893
29. Melsted P, Pritchard J (2011) Efficient counting of k-mers in dna sequences using a bloom filter. BMC Bioinformatics 12: 333. doi: 10.1186/1471-2105-12-333 PMID: 21831268
30. Salikhov K, Sacomoto G, Kucherov G (2014) Using cascading bloom filters to improve the memory usage for de brujin graphs. Algorithms for Molecular Biology 9: 2. doi: 10.1186/1748-7188-9-2 PMID: 24565280
31. Stranneheim H, Kaller M, Allander T, Andersson B, Arvestad L, et al. (2010) Classification of dna sequences using bloom filters. Bioinformatics 26: 1595-1600. doi: 10.1093/bioinformatics/btq230 PMID: 20472541
32. Chu J, Sadeghi S, Raymond A, Jackman SD, Nip KM, et al. (2014) Biobloom tools: fast, accurate and memory-efficient host species sequence screening using bloom filters. Bioinformatics 30: 3402-3404. doi: 10.1093/bioinformatics/btu558 PMID: 25143290
33. Broder A, Mitzenmacher M (2004) Network Applications of Bloom Filters: A Survey. Internet Mathematics 1: 485-509. doi: 10.1080/15427951.2004.10129096
34. Johnson DS, Garey MR (1985) A 71/60 theorem for bin packing. J Complexity: 65-106. doi: 10.1016/0885-064X(85)90022-6
35. Vazirani VV (2001) Approximation Algorithms. New York, NY, USA: Springer-Verlag New York, Inc.
36. Manber U, Myers G (1990) Suffix arrays: A new method for on-line string searches. In: Proceedings of the First Annual ACM-SIAM Symposium on Discrete Algorithms. Philadelphia, PA, USA: Society for Industrial and Applied Mathematics, SODA '90, pp. 319-327. http://dl.acm.org/citation.cfm?id=320176.320218.
37. Manber U, Myers G (1993) Suffix arrays: A new method for on-line string searches. SIAM Journal on Computing 22: 935-948. doi: 10.1137/0222058
38. Puglisi SJ, Smyth WF, Turpin AH (2007) A taxonomy of suffix array construction algorithms. ACM Comput Surv 39. doi: 10.1145/1242471.1242472
39. Ferragina P, Gagie T, Manzini G (2012) Lightweight data indexing and compression in external memory. Algorithmica 63: 707-730. doi: 10.1007/s00453-011-9535-0
40. Ferragina P, Manzini G (2000) Opportunistic data structures with applications. In: Foundations of Computer Science, 2000. Proceedings. 41st Annual Symposium on. pp. 390-398.
41. Li H (2013) Aligning sequence reads, clone sequences and assembly contigs with BWA-MEM. ArXiv eprints.
42. Needleman SB, Wunsch CD (1970) A general method applicable to the search for similarities in the amino acid sequence of two proteins. Journal of Molecular Biology 48: 443-453. doi: 10.1016/0022-2836(70)90057-4 PMID: 5420325