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Article Dans Une Revue Bioinformatics Année : 2018

Practical dynamic de Bruijn graphs

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Résumé

As datasets of DNA reads grow rapidly, it becomes more and more important to represent de Bruijn graphs compactly while still supporting fast assembly. Previous implementations have not supported edge deletion, however, which is important for pruning spurious edges from the graph. Belazzougui et al. Belazzougui et al. (2016b) recently proposed a compact and fully dynamic representation, which supports exact membership queries and insertions and deletions of both nodes and edges. In this paper we give a practical implementation of their data structure, supporting exact membership queries and insertions and deletions of edges only, and demonstrate experimentally that its performance is comparable to that of state-of-the-art implementations based on Bloom filters. Our source-code is publicly available at https://github.com/csirac/kbf under an open-source license.
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Dates et versions

hal-01935559 , version 1 (11-12-2019)

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Alan Kuhnle, Victoria G. Crawford, Christina Boucher, Rayan Chikhi, Travis Gagie. Practical dynamic de Bruijn graphs. Bioinformatics, 2018, ⟨10.1093/bioinformatics/bty500⟩. ⟨hal-01935559⟩
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