Lightweight algorithms for constructing and inverting the BWT of string collections

Theoretical Computer Science

Volumn 483, Issue , 2013, Pages 134-148

  Bauer, Markus J ^a   Cox, Anthony J ^a   Rosone, Giovanna ^b  

^a ILLUMINA INC   (United States)

^b UNIVERSITY OF PALERMO   (Italy)

Author keywords

BWT; Next generation sequencing; Text indexes

Indexed keywords

ALGORITHMS AND DATA STRUCTURES; BURROWS-WHEELER TRANSFORM; BWT; COMPUTATIONAL CHALLENGES; EXTERNAL MEMORY; NEXT-GENERATION SEQUENCING; RECENT PROGRESS; TEXT INDEXES;

ALGORITHMS; DATA PROCESSING; DATA STRUCTURES; DNA SEQUENCES; RANDOM ACCESS STORAGE;

BACKWARD WAVE TUBES;

EID: 84876410333     PISSN: 03043975     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.tcs.2012.02.002     Document Type: Article

References (25)

1. M.J. Bauer, A.J. Cox, and G. Rosone Lightweight BWT construction for very large string collections CPM 2011 LNCS vol. 6661 2011 Springer 219 231
2. D.R. Bentley Accurate whole human genome sequencing using reversible terminator chemistry Nature 456 7218 2008 53 59
3. M. Burrows, D.J. Wheeler, A block sorting data compression algorithm, Technical report, DIGITAL System Research Center, 1994.
4. A.J. Cox, O.B. Schulz-Trieglaff, I. Khrebtukova, M.J. Bauer, E.P. Murchison, Z. Ning, M. Hims, S. Luo, D.J. Evers, Poster Abstract: Hypothesis-free detection of splice junctions in RNA-Seq data, in: Proceedings of CSHL conference on Genome Informatics, 2011.
5. P. Ferragina, T. Gagie, and G. Manzini Lightweight data indexing and compression in external memory LATIN LNCS vol. 6034 2010 Springer 697 710
6. P. Ferragina, and G. Manzini Opportunistic data structures with applications Proceedings of the 41st Annual Symposium on Foundations of Computer Science 2000 IEEE Computer Society Washington, DC, USA 390 398
7. P. Ferragina, and G. Manzini Indexing compressed text J. ACM 52 2005 552 581
8. National Center for Biotechnology Information. Sequence Read Archive. http://trace.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?.
9. G.H. Gonnet, R.A. Baeza-Yates, and T. Snider New Indices for Text: PAT Trees and PAT Arrays 1992 Prentice-Hall, Inc Upper Saddle River, NJ, USA pp. 66-82
10. W.K. Hon, T.W. Lam, K. Sadakane, W.K. Sung, and S.M. Yiu A space and time efficient algorithm for constructing compressed suffix arrays Algorithmica 48 2007 23 36
11. J. Kärkkäinen Fast BWT in small space by blockwise suffix sorting Theor. Comput. Sci. 387 2007 249 257
12. J. Kärkkäinen, P. Sanders, and S. Burkhardt Linear work suffix array construction J. ACM 53 2006 918 936
13. D. Kim, J. Sim, H. Park, and K. Park Linear-time construction of suffix arrays CPM 2003 LNCS vol. 2676 2003 Springer-Verlag Berlin, Heidelberg 186 199
14. P. Ko, and S. Aluru Space efficient linear time construction of suffix arrays J. Discrete Algorithms 3 2-4 2005 143 156
15. S. Mantaci, A. Restivo, G. Rosone, and M. Sciortino An extension of the Burrows Wheeler transform and applications to sequence comparison and data compression CPM 2005 LNCS vol. 3537 2005 178 189
16. S. Mantaci, A. Restivo, G. Rosone, and M. Sciortino An extension of the Burrows-Wheeler transform Theor. Comput. Sci. 387 3 2007 298 312
17. S. Mantaci, A. Restivo, G. Rosone, and M. Sciortino A new combinatorial approach to sequence comparison Theory Comput. Syst. 42 3 2008 411 429
18. M.L. Metzker Sequencing technologies - the next generation Nature Reviews Genetics 11 1 2009 31 46
19. G. Nong, S. Zhang, and W.H. Chan Linear time suffix array construction using d-critical substrings CPM 2009 LNCS 2009 Springer-Verlag Berlin, Heidelberg 54 67
20. P.A. Pevzner, H. Tang, M.S. Waterman, A new approach to fragment assembly in DNA sequencing, in: RECOMB, 2001, pp. 256-267.
21. S.J. Puglisi, W.F. Smyth, and A.H. Turpin A taxonomy of suffix array construction algorithms ACM Comput. Surv. 39 2007
22. B.P. Walenz, R.A. Lippert, and C.M. Mobarry A space-efficient construction of the Burrows-Wheeler transform for genomic data J. Comput. Biol. 12 7 2005 943 951
23. J.T. Simpson, and R. Durbin Efficient construction of an assembly string graph using the FM-index Bioinformatics 26 12 2010 i367-i373
24. J.T. Simpson, R. Durbin, Efficient de novo assembly of large genomes using compressed data structures, Genome Research, December 2011 (in press).
25. J. Sirén Compressed suffix arrays for massive data SPIRE LNCS vol. 5721 2009 Springer 63 74