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

Graph edition is a vastly studied subject, with many heuristics to compare topologies, and many NP-hard problems. Here, we present a method, relying on the specificities of what a pangenome graph is (a collection of subsequences linked by edges, that represents the embedding of genomes inside a graph structure) to formulate a O(n) solution in this specific case. It allows us to pinpoint dissimilarities between graphs, and we can analyse how such graphs differ when build with different tools, or parameters. Warning: all graphs are given as they came out of the Minigraph-Cactus and PGGB pipelines. It means, as `rs-pancat-compare` can compare only GFA1.0 that you must perform conversion using the `vg toolkit` (see [commands available on this GitHub](https://github.com/dubssieg/pancat_paper)) Data description: Archive `yeast_dataset`: Contains the raw `.fasta` genomes used to build the yeast chromosome 1 graphs described in the publication. Archive `json_datasets_results`: Contains the computed distance, variants, and sequence complexity analysis results as `.json` files. Archive `reference_impact`: Contains the `.gfa` graphs used for the comparison of the impact of the reference choice against the secondary genome order in Minigraph-Cactus (fig 1A of the article). Archive `mgc_vs_pggb`: Contains the `.gfa` graphs used for the comparison of the impact of the reference choice in Minigraph-Cactus against PGGB (fig 1B of the article). Archives `growth_replicate_XX` (not kept in paper): These archives are replicates with varying references of an experiment made by adding more and more genomes to the graphs. The file names ranges from 2 to 15, these numbers being the number of genomes included in the graph. (Yeast dataset, chromosome 1) Archive `software_evolution` (not kept in paper): This archive contains graphs made using the same 15 genomes of yeast (chromosome 1) on three different versions of Minigraph-Cactus and three different versions of PGGB.