PanAbyss

PanAbyss is a tool to manipulate and visualize pangenomes variation graphs. It is based on a graph database modelisation (Neo4j) created from a pangenome graph (GFA file) and annotation files (GFF or GTF).

It allows, from a GFA file and annotation files (GFF or GTF) to link annotations to the pangenome, and then: (1) compute shared regions between a set of selected haplotypes, (2) compute the sequences of a selected region, (3) compute a global phylogenetic tree or a local phylogenetic tree from a selected region (neighbour joining with a distance matrix based on Jaccard index), and (4) visualize a region and annotation of the pangenome.

PanAbyss is available on INRAE Forge.