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

ABSTRACT:

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 ge

SUBMITTER: Dubois S 

PROVIDER: S-EPMC12187062 | biostudies-literature | 2025 Jun

REPOSITORIES: biostudies-literature