BubbleGun

Tool for detecting bubbles and superbubbles in De-bruijn/variation graphs. Several graph-related functions are also implemented in BubbleGun:

• Graph compacting (merging linear stretches of single nodes),
• Extracting the biggest connected component in the graph
• Separating certain chains by their id for further examination
• Extracting a user-specified neighborhood size around a node to extract as a separate graph for examination
• Extracting two random paths from each bubble chain for haplotyping
• Extracting information from long reads aligned to bubble chains

Publication and availability

Publication available here, source code available here.

Warning

The function bfs in the package starts an infinite loop if target node is on a end of the graph.

The tool, written in Python, is both usable in command-line and as imports in other Python scripts/programs.