BubbleGun: enumerating bubbles and superbubbles in genome graphs | Zendy

Fawaz Dabbaghie | Zendy; Jana Ebler | Zendy; Tobias Marschall | Zendy

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BubbleGun: enumerating bubbles and superbubbles in genome graphs

Author(s) -

Fawaz Dabbaghie,

Jana Ebler,

Tobias Marschall

Publication year - 2022

Publication title -

bioinformatics

Language(s) - English

Resource type - Journals

SCImago Journal Rank - 3.599

H-Index - 390

eISSN - 1367-4811

pISSN - 1367-4803

DOI - 10.1093/bioinformatics/btac448

Subject(s) - de bruijn sequence , computer science , genome , context (archaeology) , graph , de bruijn graph , theoretical computer science , biology , combinatorics , genetics , gene , mathematics , paleontology

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.

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