From de Bruijn graphs to variation graphs-relationships between pangenome models
Abstract
Pangenomes serve as a framework for joint analysis of genomes of related organisms. Several pangenome models were proposed, offering different functionalities, applications provided by available tools, their efficiency etc. Among them, two graph-based models are particularly widely used: variation graphs and de Bruijn graphs. In the current paper we propose an axiomatization of the desirable properties of a graph representation of a collection of strings. We show the relationship between variation graphs satisfying these criteria and de Bruijn graphs. This relationship can be used to efficiently build a variation graph representing a given set of genomes, transfer annotations between both models, compare the results of analyzes based on each model etc.
Keywords
Cite
@article{arxiv.2503.14520,
title = {From de Bruijn graphs to variation graphs-relationships between pangenome models},
author = {Adam Cicherski and Norbert Dojer},
journal= {arXiv preprint arXiv:2503.14520},
year = {2025}
}
Comments
Submitted to International Symposium on String Processing and Information Retrieval. Cham: Springer Nature Switzerland, 2023 (SPIRE2023). This preprint has not undergone peer review or any post-submission improvements or corrections. The Version of Record of this contribution is published in LNCS, volume 14240, and is available online at https://doi.org/10.1007/978-3-031-43980-3_10