Browsing by Author "Previtali, Marco"

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    Bidirectional Variable-Order de Bruijn Graphs
    (World Scientific Publishing, 2018-12) Belazzougui, Djamal; Gagie, Travis; Mäkinen, Veli; Previtali, Marco; Puglisi, Simon J.
    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.
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    Bidirectional Variable-Order de Bruijn Graphs
    (Springer International Publishing, 2016-03-22) Belazzougui, Djamal; Gagie, Travis; Mäkinen, Veli; Previtali, Marco; Puglisi, Simon J.
    Implementing de Bruijn graphs compactly is an important problem because of their role in genome assembly. There are currently two main approaches, one using Bloom filters and the other using a kind of Burrows-Wheeler Transform on the edge labels of the graph. The second representation is more elegant and can even handle many graph-orders at once, but it does not cleanly support traversing edges backwards or inserting new nodes or edges. In this paper we resolve the first of these issues and partially address the second.
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    Fully Dynamic de Bruijn Graphs
    (Springer International Publishing, 2016-09-21) Belazzougui, Djamal; Gagie, Travis; Mäkinen, Veli; Previtali, Marco
    We present a space- and time-efficient fully dynamic implementation of de Bruijn graphs, which can also support fixed-length jumbled pattern matching.