Pairwise graph edit distance characterizes the impact of the construction method on pangenome graphs - Inria - Institut national de recherche en sciences et technologies du numérique
Pré-Publication, Document De Travail Année : 2024

Pairwise graph edit distance characterizes the impact of the construction method on pangenome graphs

Résumé

Motivation: Pangenome variation graphs are an increasingly used tool to perform genome analysis, aiming to replace a linear reference in a wide variety of genomic analyses. The construction of a variation graph from a collection of chromosome-size genome sequences is a difficult task that is generally addressed using a number of heuristics. The question that arises is to what extent the construction method influences the resulting graph, and the characterization of variability. Results: We aim to characterize the differences between variation graphs derived from the same set of genomes with a metric which expresses and pinpoint differences. We designed a pairwise variation graph comparison algorithm, which establishes an edit distance between variation graphs, threading the genomes through both graphs. We applied our method to pangenome graphs built from yeast and human chromosome collections, and demonstrate that our method effectively characterizes discordances between pangenome graph construction methods and scales to real datasets.
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hal-04871087 , version 1 (07-01-2025)

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Siegfried Dubois, Matthias Zytnicki, Claire Lemaitre, Thomas Faraut. Pairwise graph edit distance characterizes the impact of the construction method on pangenome graphs. 2024. ⟨hal-04871087⟩
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