From Indexing Data Structures to de Bruijn Graphs

New technologies have tremendously increased sequencing throughput compared to traditional techniques, thereby complicating DNA assembly. Hence, assembly 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 de Bruijn graph of order $k$ from a pre-existing index, and especially a contracted version of the de Bruijn graph, where non branching paths are condensed into single nodes. Here, we formalise the relationship between suffix trees/arrays and dBGs, and exhibit linear time algorithms for constructing the full or contracted de Bruijn graphs. 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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Additional Info

Field Value
Source https://hal-lirmm.ccsd.cnrs.fr/lirmm-00950983
Author Cazaux, Bastien, Lecroq, Thierry, Rivals, Eric
Maintainer CCSD
Last Updated May 6, 2026, 03:17 (UTC)
Created May 6, 2026, 03:17 (UTC)
Identifier Report N°: RR-14004
Language en
Rights https://about.hal.science/hal-authorisation-v1/
contributor Méthodes et Algorithmes pour la Bioinformatique (MAB) ; Laboratoire d'Informatique de Robotique et de Microélectronique de Montpellier (LIRMM) ; Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)
creator Cazaux, Bastien
date 2014-02-20T00:00:00
harvest_object_id ba446b10-086d-41a2-be2e-11bdc67e544c
harvest_source_id 3374d638-d20b-4672-ba96-a23232d55657
harvest_source_title test moissonnage SELUNE
metadata_modified 2025-03-23T00:00:00
set_spec type:REPORT