BubbleGun: Enumerating Bubbles and Superbubbles in Genome Graphs

Motivation With the fast development of third generation sequencing machines, de novo genome assembly is becoming a routine even for larger genomes. Graph-based representations of genomes arise both as part of the assembly process, but also in the context of pangenomes representing a population. In both cases, polymorphic loci lead to bubble structures in such graphs. Detecting bubbles is hence an important task when working with genomic variants in the context of genome graphs. Results Here, we present a fast general-purpose tool, called BubbleGun , for detecting bubbles and superbubbles in genome graphs. Furthermore, BubbleGun detects and outputs runs of linearly connected bubbles and superbubbles, which we call bubble chains . We showcase its utility on de Bruijn graphs and compare our results to vg ’s snarl detection. We show that BubbleGun is considerably faster than vg especially in bigger graphs, where it reports all bubbles in less than 30 minutes on a human sample de Bruijn graph of around 2 million nodes. Availability BubbleGun is available and documented at https://github.com/fawaz-dabbaghieh/bubble_gun under MIT license. Contact [email protected] or [email protected] Supplementary information Supplementary data are available at Bioinformatics online.