A superbubble is a type of directed acyclic subgraph with single distinct source and sink vertices. In genome assembly and genet- ics, the possible paths through a superbubble can be considered to rep- resent the set of possible sequences at a location in a genome. Bidirected and biedged graphs are a generalization of digraphs that are increasingly being used to more fully represent genome assembly and variation prob- lems. Here we define snarls and ultrabubbles, generalizations of super- bubbles for bidirected and biedged graphs, and give an efficient algorithm for the detection of these more general structures. Key to this algorithm is the cactus graph, which we show encodes the nested decomposition of a graph into snarls and ultrabubbles within its structure. We propose and demonstrate empirically that this decomposition on bidirected and biedged graphs solves a fundamental problem by defining genetic sites for any collection of genomic variations, including complex structural vari- ations, without need for any single reference genome coordinate system. Furthermore, the nesting of the decomposition gives a natural way to describe and model variations contained within large variations, a case not currently dealt with by existing formats, e.g. VCF.
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