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From de Bruijn graphs to variation graphs-relationships between pangenome models https://arxiv.org/abs/2503.14520 #qbioGN #mathCO

From de Bruijn graphs to variation graphs-relationships between pangenome models

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.

arXiv.org
March 21, 2025 at 3:25 AM · · feed2toot · 0 · 0 · 0
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