Benchmark datasets for BubbleFinder: ultrabubble detection in pangenome graphs

Pangenome graph files (GFA and GBZ formats) used for benchmarking ultrabubble detection tools in the paper 'Scalable computation of ultrabubbles in pangenomes by orienting bidirected graphs'. Includes pggb graphs, 1000GP variation graphs, de Bruijn graphs, and Pangene graphs. Note: The HPRC Minigraph-Cactus pangenome graphs used in the benchmarks (hprc-v1.1-mc-chm13 and hprc-v2.0-mc-chm13, in GFA and GBZ formats) are not included in this deposit due to their large size. They can be downloaded from the official HPRC pangenome resources at https://github.com/human-pangenomics/hpp_pangenome_resources. Direct download links: - hprc-v1.1-mc-chm13.gfa.gz: https://s3-us-west-2.amazonaws.com/human-pangenomics/pangenomes/freeze/freeze1/minigraph-cactus/hprc-v1.1-mc-chm13/hprc-v1.1-mc-chm13.gfa.gz- hprc-v1.1-mc-chm13.gbz: https://s3-us-west-2.amazonaws.com/human-pangenomics/pangenomes/freeze/freeze1/minigraph-cactus/hprc-v1.1-mc-chm13/hprc-v1.1-mc-chm13.gbz - hprc-v2.0-mc-chm13.gfa.gz: https://s3-us-west-2.amazonaws.com/human-pangenomics/pangenomes/scratch/2025_02_28_minigraph_cactus/hprc-v2.0-mc-chm13/hprc-v2.0-mc-chm13.gfa.gz - hprc-v2.0-mc-chm13.gbz: https://s3-us-west-2.amazonaws.com/human-pangenomics/pangenomes/scratch/2025_02_28_minigraph_cactus/hprc-v2.0-mc-chm13/hprc-v2.0-mc-chm13.gbz