Abstract
A modern DNA sequencing machine can generate a billion or more sequence fragments in a matter of days. The many uses of the BWT in compression and indexing are well known, but the computational demands of creating the BWT of datasets this large have prevented its applications from being widely explored in this context.
We address this obstacle by presenting two algorithms capable of computing the BWT of very large string collections. The algorithms are lightweight in that the first needs O(m logm) bits of memory to process m strings and the memory requirements of the second are constant with respect to m.
We evaluate our algorithms on collections of up to 1 billion strings and compare their performance to other approaches on smaller datasets. Although our tests were on collections of DNA sequences of uniform length, the algorithms themselves apply to any string collection over any alphabet.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
Preview
Unable to display preview. Download preview PDF.
References
Adjeroh, D., Bell, T., Mukherjee, A.: The Burrows-Wheeler Transform: Data Compression, Suffix Arrays, and Pattern Matching, 1st edn. Springer, Heidelberg (2008)
Bentley, D.R., et al.: Accurate whole human genome sequencing using reversible terminator chemistry. Nature 456(7218), 53–59 (2008)
Ferragina, P., Gagie, T., Manzini, G.: Lightweight data indexing and compression in external memory. In: López-Ortiz, A. (ed.) LATIN 2010. LNCS, vol. 6034, pp. 697–710. Springer, Heidelberg (2010)
Ferragina, P., Manzini, G.: Opportunistic data structures with applications. In: Proceedings of the 41st Annual Symposium on Foundations of Computer Science, Washington, DC, USA, pages 390. IEEE Computer Society, Los Alamitos (2000)
Ferragina, P., Manzini, G.: Indexing compressed text. J. ACM 52, 552–581 (2005)
National Center for Biotechnology Information. Sequence Read Archive, http://trace.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?
Gonnet, G.H., Baeza-Yates, R.A., Snider, T.: New indices for text: PAT Trees and PAT arrays, pp. 66–82. Prentice-Hall, Inc., Upper Saddle River (1992)
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, 23–36 (2007)
Kärkkäinen, J., Sanders, P., Burkhardt, S.: Linear work suffix array construction. J. ACM 53, 918–936 (2006)
Kim, D., Sim, J., Park, H., Park, K.: Linear-time construction of suffix arrays. In: Baeza-Yates, R., Chávez, E., Crochemore, M. (eds.) CPM 2003. LNCS, vol. 2676, pp. 186–199. Springer, Heidelberg (2003)
Ko, P., Aluru, S.: Space efficient linear time construction of suffix arrays. Journal of Discrete Algorithms 3(2-4), 143–156 (2005)
Mantaci, S., Restivo, A., Rosone, G., Sciortino, M.: An extension of the burrows wheeler transform and applications to sequence comparison and data compression. In: Apostolico, A., Crochemore, M., Park, K. (eds.) CPM 2005. LNCS, vol. 3537, pp. 178–189. Springer, Heidelberg (2005)
Mantaci, S., Restivo, A., Rosone, G., Sciortino, M.: An extension of the Burrows-Wheeler Transform. Theor. Comput. Sci. 387(3), 298–312 (2007)
Mantaci, S., Restivo, A., Rosone, G., Sciortino, M.: A new combinatorial approach to sequence comparison. Theory Comput. Syst. 42(3), 411–429 (2008)
Metzker, M.L.: Sequencing technologies – the next generation. Nature Reviews Genetics 11(1), 31–46 (2009)
Nong, G., Zhang, S., Chan, W.H.: Linear time suffix array construction using d-critical substrings. In: Kucherov, G., Ukkonen, E. (eds.) CPM 2009 Lille. LNCS, vol. 5577, pp. 54–67. Springer, Heidelberg (2009)
Puglisi, S.J., Smyth, W.F., Turpin, A.H.: A taxonomy of suffix array construction algorithms. ACM Comput. Surv. 39 (July 2007)
Walenz, B.P., Lippert, R.A., Mobarry, C.M.: A Space-Efficient Construction of the Burrows-Wheeler Transform for Genomic Data. Journal of Computational Biology 12(7), 943–951 (2005)
Simpson, J.T., Durbin, R.: Efficient construction of an assembly string graph using the FM-index. Bioinformatics 26(12), i367–i373 (2010)
Sirén, J.: Compressed suffix arrays for massive data. In: Karlgren, J., Tarhio, J., Hyyrö, H. (eds.) SPIRE 2009. LNCS, vol. 5721, pp. 63–74. Springer, Heidelberg (2009)
Author information
Authors and Affiliations
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2011 Springer-Verlag Berlin Heidelberg
About this paper
Cite this paper
Bauer, M.J., Cox, A.J., Rosone, G. (2011). Lightweight BWT Construction for Very Large String Collections. In: Giancarlo, R., Manzini, G. (eds) Combinatorial Pattern Matching. CPM 2011. Lecture Notes in Computer Science, vol 6661. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-642-21458-5_20
Download citation
DOI: https://doi.org/10.1007/978-3-642-21458-5_20
Publisher Name: Springer, Berlin, Heidelberg
Print ISBN: 978-3-642-21457-8
Online ISBN: 978-3-642-21458-5
eBook Packages: Computer ScienceComputer Science (R0)