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Updated: Sep 5, 2025

A Femtoliter Droplet Array for Massively Parallel Protein Synthesis from Single DNA Molecules

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Published on: June 20, 2020

BubbleGun: enumerating bubbles and superbubbles in genome graphs.

Fawaz Dabbaghie^1,2, Jana Ebler¹, Tobias Marschall¹

¹Medical Faculty, Institute for Medical Biometry and Bioinformatics, Heinrich Heine University Düsseldorf, Düsseldorf 40225, Germany.

Bioinformatics (Oxford, England)

|July 8, 2022

Summary

This summary is machine-generated.

BubbleGun efficiently detects complex bubble structures and bubble chains in genome graphs, crucial for analyzing genomic variants and pangenomes. This tool significantly speeds up analysis, especially for large datasets like human genomes.

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Last Updated: Sep 5, 2025

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Published on: June 20, 2020

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Published on: May 23, 2018

Area of Science:

Genomics
Bioinformatics

Background:

Advancements in sequencing technology enable accurate de novo genome assembly for large genomes.
Graph-based genome representations are essential for genome assembly and pangenomics.
Polymorphic loci in genome graphs manifest as bubble structures, requiring detection for variant analysis.

Purpose of the Study:

To develop a fast, general-purpose tool for detecting bubbles, superbubbles, and bubble chains in genome graphs.
To provide an efficient solution for analyzing genomic variants within graph structures.

Main Methods:

Implementation of BubbleGun as a Python3 package.
Utilizing de Bruijn graphs for testing and comparison.
Comparing BubbleGun's performance against existing tools like vg for snarl detection.

Main Results:

BubbleGun effectively detects bubbles, superbubbles, and bubble chains in genome graphs.
BubbleGun demonstrates considerable speed improvements over vg, especially on larger graphs.
BubbleGun processed a human sample de Bruijn graph (approx. 2 million nodes) in under 30 minutes.

Conclusions:

BubbleGun is a fast and efficient tool for identifying complex variant structures in genome graphs.
The tool aids in the analysis of genomic variants and pangenomes.
BubbleGun offers a significant performance advantage for large-scale genomic analyses.