Comparing DNA sequence collections by direct comparison of compressed text indexes

Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)

Volumn 7534 LNBI, Issue , 2012, Pages 214-224

  Cox, Anthony J ^a   Jakobi, Tobias ^b   Rosone, Giovanna ^c   Schulz Trieglaff, Ole B ^a  

^a ILLUMINA INC   (United States)

^b BIELEFELD UNIVERSITY   (Germany)

^c UNIVERSITY OF PALERMO   (Italy)

Author keywords

[No Author keywords available]

Indexed keywords

BURROWS-WHEELER TRANSFORM; EXTERNAL MEMORY; GENOMIC DATA SETS; QUERY SEQUENCE; SEQUENCE ALIGNMENTS; SPLICE JUNCTIONS; STRUCTURE-BASED;

ALGORITHMS; BACKWARD WAVE TUBES; DATA STRUCTURES; GENES; INDEXING (OF INFORMATION); RANDOM ACCESS STORAGE;

BIOINFORMATICS;

EID: 84866722538     PISSN: 03029743     EISSN: 16113349     Source Type: Book Series    
DOI: 10.1007/978-3-642-33122-0_17     Document Type: Conference Paper

References (17)

1. Abouelhoda, M.I., Kurtz, S., Ohlebusch, E.: Replacing suffix trees with enhanced suffix arrays. Journal of Discrete Algorithms 2(1), 53-86 (2004)
2. Adjeroh, D., Bell, T., Mukherjee, A.: The Burrows-Wheeler Transform: Data Compression, Suffix Arrays, and Pattern Matching, 1st edn. Springer Publishing Company, Incorporated (2008)
3. Bauer, M.J., Cox, A.J., Rosone, G.: Lightweight BWT Construction for Very Large String Collections. In: Giancarlo, R., Manzini, G. (eds.) CPM 2011. LNCS, vol. 6661, pp. 219-231. Springer, Heidelberg (2011)
4. Bauer, M.J., Cox, A.J., Rosone, G., Lightweight algorithms for constructing and inverting the BWT of string collections, Theoretical Computer Science,Volume 483, page 134-148, 2012.
5. Burrows, M., Wheeler, D.J.: A block sorting data compression algorithm. Technical report, DIGITAL System Research Center (1994)
6. Cox, A.J., Bauer, M.J., Jakobi, T., Rosone, G.: Large-scale compression of genomic sequence databases with the Burrows-Wheeler transform. Bioinformatics 28(11), 1415-1419 (2012)
7. Ferragina, P., Manzini, G.: Opportunistic data structures with applications. In: Proceedings of the 41st Annual Symposium on Foundations of Computer Science, pp. 390-398. IEEE Computer Society, Washington, DC (2000)
8. Langmead, B., Trapnell, C., Pop, M., Salzberg, S.: Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biology 10(3), R25+ (2009)
9. Li, H., Durbin, R.: Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics 25(14), 1754-1760 (2009)
10. Li, R., Yu, C., Li, Y., Lam, T.W., Yiu, S.M., Kristiansen, K., Wang, J.: Soap2: an improved ultrafast tool for short read alignment. Bioinformatics 25(15), 1966-1967 (2009)
11. Mantaci, S., Restivo, A., Rosone, G., Sciortino, M.: An extension of the Burrows-Wheeler Transform. Theor. Comput. Sci. 387(3), 298-312 (2007)
12. Murchison, E.P., Schulz-Trieglaff, O.B., Ning, Z., Alexandrov, L.B., Bauer, M.J., Fu, B., Hims, M., Ding, Z., Ivakhno, S., Stewart, C., Ng, B.L., Wong, W., Aken, B., White, S., Alsop, A., Becq, J., Bignell, G.R., Cheetham, R.K., Cheng, W., Connor, T.R., Cox, A.J., Feng, Z., Gu, Y., Grocock, R.J., Harris, S.R., Khrebtukova, I., Kingsbury, Z., Kowarsky, M., Kreiss, A., Luo, S., Marshall, J., McBride, D.J., Murray, L., Pearse, A., Raine, K., Rasolonjatovo, I., Shaw, R., Tedder, P., Tregidgo, C., Vilella, A.J., Wedge, D.C., Woods, G.M., Gormley, N., Humphray, S., Schroth, G., Smith, G., Hall, K., Searle, S.M.J., Carter, N.P., Papenfuss, A.T., Futreal, P.A., Campbell, P.J., Yang, F., Bentley, D.R., Evers, D.J., Stratton, M.R.: Genome sequencing and analysis of the tasmanian devil and its transmissible cancer. Cell 148(4), 780-791 (2012)
13. Navarro, G., Mäkinen, V.: Compressed full-text indexes. ACM Comput. Surv. 39(1) (2007)
14. Quinlan, A.R., Hall, I.M.: Bedtools: a flexible suite of utilities for comparing genomic features. Bioinformatics 26(6), 841-842 (2010)
15. Simpson, J.T., Durbin, R.: Efficient construction of an assembly string graph using the FM-index. Bioinformatics 26(12), i367-i373 (2010)
16. Simpson, J.T., Durbin, R.: Efficient de novo assembly of large genomes using compressed data structures. Genome Research 22(3), 549-556 (2011)
17. Trapnell, C., Pachter, L., Salzberg, S.L.: Tophat: discovering splice junctions with rna-seq. Bioinformatics 25(9), 1105-1111 (2009)