From Indexing Data Structures to de Bruijn Graphs

Abstract : New technologies have tremendously increased sequencing throughput com-pared to traditional techniques, thereby complicating DNA assembly. Hence, as-sembly programs resort to de Bruijn graphs (dBG) of k-mers of short reads to compute a set of long contigs, each being a putative segment of the sequenced molecule. Other types of DNA sequence analysis, as well as preprocessing of the reads for assembly, use classical data structures to index all substrings of the reads. It is thus interesting to exhibit algorithms that directly build a dBG of order k from a pre-existing index, and especially a contracted version of the dBG, where non branching paths are condensed into single nodes. Here, we formalise the relation-ship between suffix trees/arrays and dBGs, and exhibit linear time algorithms for constructing the full or contracted dBGs. Finally, we provide hints explaining why this bridge between indexes and dBGs enables to dynamically update the order k of the graph.
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https://hal-lirmm.ccsd.cnrs.fr/lirmm-01081429
Contributor : Eric Rivals <>
Submitted on : Friday, November 7, 2014 - 5:47:40 PM
Last modification on : Thursday, July 11, 2019 - 9:48:26 AM
Long-term archiving on : Sunday, February 8, 2015 - 11:11:43 AM

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Bastien Cazaux, Thierry Lecroq, Eric Rivals. From Indexing Data Structures to de Bruijn Graphs. CPM: Combinatorial Pattern Matching, Moscow State University, Jun 2014, Moscow, Russia. pp.89-99, ⟨10.1007/978-3-319-07566-2_10⟩. ⟨lirmm-01081429⟩

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