BubbleGun: enumerating bubbles and superbubbles in genome graphs.

ABSTRACT:

Motivation

With the fast development of sequencing technology, accurate de novo genome assembly is now possible 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

SUBMITTER: Dabbaghie F 

PROVIDER: S-EPMC9438957 | biostudies-literature | 2022 Sep

REPOSITORIES: biostudies-literature