Abstract
In the life sciences, determining the sequence of bio-molecules is essential step towards the understanding of their functions and interactions inside an organism. Powerful technologies allows to get huge quantities of short sequencing reads that need to be assemble to infer the complete target sequence. These constraints favour the use of a version de Bruijn Graph (DBG) dedicated to assembly. The de Bruijn Graph is usually built directly from the reads, which is time and space consuming. Given a set \(R\) of input words, well-known data structures, like the generalised suffix tree, can index all the substrings of words in \(R\). In the context of DBG assembly, only substrings of length \(k+1\) and some of length \(k\) are useful. A truncated version of the suffix tree can index those efficiently. As indexes are exploited for numerous purposes in bioinformatics, as read cleaning, filtering, or even analysis, it is important to enable the community to reuse an existing index to build the DBG directly from it. In an earlier work we provided the first algorithms when starting from a suffix tree or suffix array. Here, we exhibit an algorithm that exploits a reduced version of the truncated suffix tree and computes the DBG from it. Importantly, a variation of this algorithm is also shown to compute the contracted DBG, which offers great benefits in practice. Both algorithms are linear in time and space in the size of the output.
This work is supported by ANR Colib’read (http://colibread.inria.fr) (ANR-12-BS02-0008) and by Défi MASTODONS SePhHaDe (http://www.lirmm.fr/mastodons) from CNRS.
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
Apostolico, A.: The myriad virtues of suffix trees. In: Apostolico, A., Galil, Z. (eds.) Combinatorial Algorithms on Words. NATO Advanced Science Institutes. Series F, vol. 12, pp. 85–96. Springer (1985)
Bowe, A., Onodera, T., Sadakane, K., Shibuya, T.: Succinct de Bruijn graphs. In: Raphael, B., Tang, J. (eds.) WABI 2012. LNCS, vol. 7534, pp. 225–235. Springer, Heidelberg (2012)
de Bruijn, N.: On bases for the set of integers. Publ. Math. Debr. 1, 232–242 (1950)
Cazaux, B., Lecroq, T., Rivals, E.: From indexing data structures to de Bruijn graphs. In: Kulikov, A.S., Kuznetsov, S.O., Pevzner, P. (eds.) CPM 2014. LNCS, vol. 8486, pp. 89–99. Springer, Heidelberg (2014)
Chikhi, R., Rizk, G.: Space-efficient and exact de Bruijn graph representation based on a Bloom filter. Algorithms for Molecular Biology 8, 22 (2013)
Conway, T.C., Bromage, A.J.: Succinct data structures for assembling large genomes. Bioinformatics 27(4), 479–486 (2011)
Golovnev, A., Kulikov, A.S., Mihajlin, I.: Approximating shortest superstring problem using de Bruijn graphs. In: Fischer, J., Sanders, P. (eds.) CPM 2013. LNCS, vol. 7922, pp. 120–129. Springer, Heidelberg (2013)
Gusfield, D.: Algorithms on strings, trees and sequences: computer science and computational biology. Cambridge University Press, Cambridge (1997)
McCreight, E.: A space-economical suffix tree construction algorithm. J. of Association for Computing Machinery 23(2), 262–272 (1976)
Na, J.C., Apostolico, A., Iliopoulos, C.S., Park, K.: Truncated suffix trees and their application to data compression. Theoretical Computer Science 304(1–3), 87–101 (2003)
Peng, Y., Leung, H.C.M., Yiu, S.M., Chin, F.Y.L.: IDBA – A practical iterative de Bruijn graph de novo assembler. In: Berger, B. (ed.) RECOMB 2010. LNCS, vol. 6044, pp. 426–440. Springer, Heidelberg (2010)
Pevzner, P., Tang, H., Waterman, M.: An Eulerian path approach to DNA fragment assembly. Proc. Natl. Acad. Sci. USA 98(17), 9748–9753 (2001)
Philippe, N., Salson, M., Commes, T., Rivals, E.: CRAC: an integrated approach to the analysis of RNA-seq reads. Genome Biology 14(3), R30 (2013)
Rizk, G., Gouin, A., Chikhi, R., Lemaitre, C.: Mindthegap: integrated detection and assembly of short and long insertions. Bioinformatics (2014)
Salmela, L.: Correction of sequencing errors in a mixed set of reads. Bioinformatics 26(10), 1284–1290 (2010)
Schulz, M.H., Bauer, S., Robinson, P.N.: The generalised k-truncated suffix tree for time-and space-efficient searches in multiple DNA or protein sequences. International J. of Bioinformatics Research and Applications 4(1), 81–95 (2008)
Author information
Authors and Affiliations
Corresponding author
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2015 Springer International Publishing Switzerland
About this paper
Cite this paper
Cazaux, B., Lecroq, T., Rivals, E. (2015). Construction of a de Bruijn Graph for Assembly from a Truncated Suffix Tree. In: Dediu, AH., Formenti, E., Martín-Vide, C., Truthe, B. (eds) Language and Automata Theory and Applications. LATA 2015. Lecture Notes in Computer Science(), vol 8977. Springer, Cham. https://doi.org/10.1007/978-3-319-15579-1_8
Download citation
DOI: https://doi.org/10.1007/978-3-319-15579-1_8
Published:
Publisher Name: Springer, Cham
Print ISBN: 978-3-319-15578-4
Online ISBN: 978-3-319-15579-1
eBook Packages: Computer ScienceComputer Science (R0)