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Published in

World Scientific Publishing, International Journal of Foundations of Computer Science, 08(29), p. 1279-1295, 2018

DOI: 10.1142/s0129054118430037

Springer Verlag, Lecture Notes in Computer Science, p. 164-178

DOI: 10.1007/978-3-662-49529-2_13

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Bidirectional Variable-Order de Bruijn Graphs

This paper was not found in any repository, but could be made available legally by the author.
This paper was not found in any repository, but could be made available legally by the author.

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Abstract

Compressed suffix trees and bidirectional FM-indexes can store a set of strings and support queries that let us explore the set of substrings they contain, adding and deleting characters on both the left and right, but they can use much more space than a de Bruijn graph for the strings. Bowe et al.’s BWT-based de Bruijn graph representation (Proc. Workshop on Algorithms for Bioinformatics, pp. 225–235, 2012) can be made bidirectional as well, at the cost of increasing its space usage by a small constant, but it fixes the length of the substrings. Boucher et al. (Proc. Data Compression Conference, pp. 383–392, 2015) generalized Bowe et al.’s representation to support queries about variable-length substrings, but at the cost of bidirectionality. In this paper we show how to make Boucher et al.’s variable-order implementation of de Bruijn graphs bidirectional.