Scalable and versatile k-mer indexing for high-throughput sequencing data

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

Volumn 7875 LNBI, Issue , 2013, Pages 237-248

  Välimäki, Niko ^a   Rivals, Eric ^b  

^a UNIVERSITY OF HELSINKI   (Finland)

^b LIRMM   (France)

Author keywords

[No Author keywords available]

Indexed keywords

HIGH-THROUGHPUT SEQUENCING; MAIN-MEMORY; NEAR-OPTIMAL; QUERY TIME; SCALE-UP; SEQUENCE ASSEMBLIES;

BIOINFORMATICS; DATA STRUCTURES; ERROR CORRECTION;

INDEXING (OF INFORMATION);

EID: 84883391439     PISSN: 03029743     EISSN: 16113349     Source Type: Book Series    
DOI: 10.1007/978-3-642-38036-5_24     Document Type: Conference Paper

References (25)

1. 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)
2. Beller, T., Gog, S., Ohlebusch, E., Schnattinger, T.: Computing the longest common prefix array based on the burrows-wheeler transform. In: Grossi, R., Sebastiani, F., Silvestri, F. (eds.) SPIRE 2011. LNCS, vol. 7024, pp. 197-208. Springer, Heidelberg (2011)
3. Burkhardt, S., Crauser, A., Ferragina, P., Lenhof, H.-P., Rivals, E., Vingron, M.: q-gram Based Database Searching Using a Suffix Array (QUASAR). In: 3rd Int. Conf. on Computational Molecular Biology, pp. 77-83. ACM Press (1999)
4. Chikhi, R., Lavenier, D.: Localized genome assembly from reads to scaffolds: Practical traversal of the paired string graph. In: Przytycka, T.M., Sagot, M.-F. (eds.) WABI 2011. LNCS, vol. 6833, pp. 39-48. Springer, Heidelberg (2011)
5. Claude, F., Fariña, A., Martínez-Prieto, M.A., Navarro, G.: Compressed q-gram indexing for highly repetitive biological sequences. In: Proc. 10th IEEE Intl. Conf. on Bioinformatics and Bioengineering, pp. 86-91 (2010)
6. Conway, T.C., Bromage, A.J.: Succinct Data Structures for Assembling Large Genomes. Bioinformatics 27(4), 479-486 (2011)
7. Ferragina, P., Manzini, G.: Opportunistic data structures with applications. In: Proc. 41st Annual Symposium on Foundations of Computer Science (FOCS), pp. 390-398. IEEE Computer Society (2000)
8. Fischer, J., Mäkinen, V., Navarro, G.: Faster entropy-bounded compressed suffix trees. Theor. Comput. Sci. 410(51), 5354-5364 (2009)
9. Grossi, R., Gupta, A., Vitter, J.S.: High-order entropy-compressed text indexes. In: 14th Ann. ACM-SIAM Symp. on Discrete Algorithms, pp. 841-850 (2003)
10. Hazelhurst, S., Lipták, Z.: Kaboom! a new suffix array based algorithm for clustering expression data. Bioinformatics 27(24), 3348-3355 (2011)
11. Hon, W.-K., Lam, T.-W., Sadakane, K., Sung,W.-K., Yiu, S.-M.: A space and time efficient algorithm for constructing compressed suffix arrays. Algorithmica 48(1), 23-36 (2007)
12. Hon, W.-K., Sadakane, K.: Space-economical algorithms for finding maximal unique matches. In: Apostolico, A., Takeda, M. (eds.) CPM 2002. LNCS, vol. 2373, pp. 144-152. Springer, Heidelberg (2002)
13. Hon, W.-K., Shah, R., Vitter, J.S.: Space-efficient framework for top-k string retrieval problems. In: FOCS, pp. 713-722. IEEE Computer Society (2009)
14. Jacobson, G.: Succinct Static Data Structures. PhD thesis, Carnegie-Mellon (1989)
15. Li, H.: Implementation of BCR, https://github.com/lh3/ropebwt
16. Li, H., Durbin, R.: Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics 25(14), 1754-1760 (2009)
17. Marçais, G., Kingsford, C.: A fast, lock-free approach for efficient parallel counting of occurrences of k-mers. Bioinformatics 27(6), 764-770 (2011)
18. Melsted, P., Pritchard, J.: Efficient counting of k-mers in dna sequences using a bloom filter. BMC Bioinformatics 12(1), 333 (2011)
19. Navarro, G., Mäkinen, V.: Compressed full-text indexes. ACM Comput. Surv. 39(1) (2007)
20. Philippe, N., Salson, M., Commes, T., Rivals, E.: CRAC: an integrated approach to read analysis. Genome Biology (in press, 2013)
21. Philippe, N., Salson, M., Lecroq, T., Léonard, M., Commes, T., Rivals, E.: Querying large read collections in main memory: a versatile data structure. BMC Bioinformatics 12, 242 (2011)
22. Rizk, G., Lavenier, D., Chikhi, R.: DSK: k-mer counting with very low memory usage. Bioinformatics, page Advance access (January 2013)
23. Salmela, L., Schröder, J.: Correcting errors in short reads by multiple alignments. Bioinformatics 27(11), 1455-1461 (2011)
24. Sirén, J.: Compressed Full-Text Indexes for Highly Repetitive Collections. PhD thesis, Dept. of Computer Science, Report A-2012-5, University of Helsinki (2012)
25. Willard, D.E.: Log-logarithmic worst-case range queries are possible in space Theta(N). Inf. Process. Lett. 17(2), 81-84 (1983)