Reconciling and Comparing Variation Graphs Using Homology Relations

Lisiecka, Anna; Cicherski, Adam; Dojer, Norbert

doi:10.4230/LIPIcs.WABI.2026.29

Abstract

In variation graphs genomic sequences are represented as paths sharing their nodes in homologous regions. Shared nodes must represent identical sequence fragments, but the definition does not impose strict criteria on when the paths should be merged and when not. Consequently, most variation graph building tools heuristically infer the graph structure from pairwise genome alignments or the results of seeding procedures of alignment algorithms.
In the current paper we introduce the concept of homology relation induced by a variation graph on the nucleotides of represented genomic sequences. This notion can be used to specify in a mathematically rigorous way the criteria the structure of a variation graph should meet. We investigate the relationships between the structures of variation graphs and their homology relations, as well as between operations on relations and on graphs. In particular, we show how to use the result of combining relations induced by different graphs to combine these graphs. Then, we propose homology-based methods of reconciling and comparing variation graphs representing the same genome collection. Moreover, we provide an implementation of homology-based tools for variation graph analysis.

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Anna Lisiecka, Adam Cicherski, and Norbert Dojer. Reconciling and Comparing Variation Graphs Using Homology Relations. In 26th International Conference on Algorithms for Bioinformatics (WABI 2026). Leibniz International Proceedings in Informatics (LIPIcs), Volume 390, pp. 29:1-29:15, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2026) https://doi.org/10.4230/LIPIcs.WABI.2026.29

Author Details

Anna Lisiecka

Institute of Informatics, University of Warsaw, Poland

Adam Cicherski

Institute of Informatics, University of Warsaw, Poland

Norbert Dojer

Institute of Informatics, University of Warsaw, Poland

Funding

This work was supported by the National Science Centre, Poland, under grant number 2022/47/B/ST6/03154.

Supplementary Materials

Software https://github.com/anialisiecka/vgrecon/ browse archived version

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Reconciling and Comparing Variation Graphs Using Homology Relations

Authors Anna Lisiecka , Adam Cicherski , Norbert Dojer

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