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Contig Model for Variable-Order de Bruijn Graphs

Authors Diego Díaz-Domínguez , Pierfrancesco Martinello , Taku Onodera, Simon J. Puglisi , Leena Salmela

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ACM Subject Classification
  • Applied computing → Bioinformatics
  • Applied computing → Molecular sequence analysis
  • Theory of computation → Data structures design and analysis
  • Applied computing → Computational genomics
Keywords
  • genome assembly
  • de Bruijn Graph
  • long reads

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Abstract

Choosing an order for constructing a de Bruijn graph (DBG) is a crucial step in de novo assembly, as no single value allows complete genome reconstruction. The variable-order de Bruijn graph (voDBG) addresses this limitation by combining DBGs of multiple orders in a single structure connected by contextual relationships. This representation enables new connections to be identified or ambiguities to be resolved during assembly. However, voDBGs currently lack a formal definition of contigs.
In this paper, we give the first formal definition of contigs for voDBGs. We show that, for a frequency range [𝓁,h] with 𝓁 > h/2, nodes whose labels occur with frequency f ∈ [𝓁, h] in the reads spell sequences of the genome with high probability under uniform sampling assumptions. We call these sequences (𝓁,h)-tigs. We also present an efficient algorithm to enumerate (𝓁,h)-tigs from a voDBG that accounts for homopolymer errors. Experiments on PacBio HiFi data show that our method significantly improves contiguity compared to unitigs in fixed-order DBGs while remaining considerably lighter than full genome assemblers.

Cite As Get BibTex

Diego Díaz-Domínguez, Pierfrancesco Martinello, Taku Onodera, Simon J. Puglisi, and Leena Salmela. Contig Model for Variable-Order de Bruijn Graphs. In 26th International Conference on Algorithms for Bioinformatics (WABI 2026). Leibniz International Proceedings in Informatics (LIPIcs), Volume 390, pp. 4:1-4:19, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2026) https://doi.org/10.4230/LIPIcs.WABI.2026.4

Author Details

Diego Díaz-Domínguez
  • Department of Computer Science, University of Helsinki, Finland
Pierfrancesco Martinello
  • Department of Computer Science, University of Helsinki, Finland
Taku Onodera
  • Graduate School of Information Science and Technology, University of Tokyo, Japan
Simon J. Puglisi
  • Department of Computer Science, University of Helsinki, Finland
Leena Salmela
  • Department of Computer Science, University of Helsinki, Finland

Funding

  • Díaz-Domínguez, Diego: supported by EU Horizon Europe grant No 101060011 and Research Council of Finland via grant 323233.
  • Martinello, Pierfrancesco: supported by Research Council of Finland via grant 370538.
  • Onodera, Taku: supported by Research Council of Finland via grant 323233.
  • Salmela, Leena: supported by Research Council of Finland via grants 323233 and 370538.

Supplementary Materials

References

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