Benchmark datasets for Billi: Panbubble and hairpin detection in pangenome graphs

Panngenome graph files (GFA format) used for benchmarking panbubble and hairpin detection in the paper Billi: Provably Accurate and Scalable Bubble Detection in Pangenome Graphs. Includes minigraph pangenome graphs and pangene gene graphs. Note: The HPRC Minigraph-Cactus pangenome graphs (hprc-v1.1-mc-chm13 and hprc-v2.0-mc-chm13) and chromosome-level graphs (chrX and chrY) are not included due to their large size. The chromosome-level graphs (chrX, chrY) are available as .vg files and must be converted to GFA format using vg. 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-v2.0-mc-chm13.gfa.gz: https://human-pangenomics.s3.amazonaws.com/pangenomes/scratch/2025_02_28_minigraph_cactus/hprc-v2.0-mc-chm13/hprc-v2.0-mc-chm13.gfa.gz chrX.vg: https://human-pangenomics.s3.amazonaws.com/pangenomes/scratch/2025_02_28_minigraph_cactus/hprc-v2.0-mc-chm13/hprc-v2.0-mc-chm13.chroms/chrX.vg chrY.vg: https://human-pangenomics.s3.amazonaws.com/pangenomes/scratch/2025_02_28_minigraph_cactus/hprc-v2.0-mc-chm13/hprc-v2.0-mc-chm13.chroms/chrY.vg Vg command to convert .vg to .gfa format: vg view input.vg > output.gfa