Enumerating Bubbles: Listing Pairs of Vertex Disjoint Paths

Abstract

Polymorphisms in DNA- or RNA-seq data lead to recognisable patterns in a de Bruijn graph representation of the reads obtained by sequencing. Such patterns have been called mouths, or bubbles in the literature. They correspond to two vertex-disjoint directed paths between a source $s$ and a target $t$. Due to the high number of such bubbles that may be present in real data, their enumeration is a major issue concerning the efficiency of dedicated algorithms. We propose the first linear delay algorithm to enumerate all bubbles with a given source, by properly transforming the graph in input and enumerating special cycles.