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Éloi Durant, François Sabot, Matthieu Conte, Mathieu Rouard (Univ Montpellier - IRD, Montpellier, France; Syngenta Seeds SAS, Saint-Sauveur, France; Bioversity International, Montpellier, France; IFB - South Green Bioinformatics Platform, Montpellier, France)
"Pangenome" may have different meanings: some might call it the full set of genes within a species, while others focus on DNA sequences and their succession in the genomes of a group of indiviuals. This second definition is often represented as genome graphs, where nodes of DNA sequences are linked together according to existing genomes, creating junctions for every variations. These representations may be difficult to understand for a human eye, as all the junctions can create visual 'noise', disrupting one's attention and hiding information. Instead of representing those as graphs, we suggest displaying them in a linear fashion, easier to parse and explore. Pangenomes could be fragmented into pangenomic blocks that might be shared between genomes, and then ordered on a single thread. We therefore introduce Panache (Pangenome Analyzer with Chromosomal Exploration), our attempt at displaying such linearized pangenomes. It displays a presence/absence matrix of pangenomic blocks and can provide additional information using a set of parallel tracks, similarly to a genome browser.