Experiment pipelines for BubbleFinder, a tool for computing bubble-like structures (snarls, superbubbles, ultrabubbles) in pangenomic graphs.
| Paper | Entry point | README |
|---|---|---|
| Identifying all snarls and superbubbles in linear-time, via a unified SPQR-tree framework | Snakefile + datasets.yaml |
snarls-superbubbles/ |
| Scalable computation of ultrabubbles in pangenomes by orienting bidirected graphs (preprint forthcoming) | run_benchmarks.sh |
ultrabubbles/ |
Both benchmarks share parts of the codebase (Snakemake modules, helper scripts, conda environments).