Hub labeling makes exact distance calculation practical for large human pangenome graphs

Hub labeling of large snarls in human chromosome pangenome graphs enables exact minimum-distance queries while indexing every snarl in 0.9–3.0 GB at a snarl limit of 500.

• Why it matters: Dense all-pairs distance matrices in the vg-style snarl index become quadratic in snarl size, making whole-genome pangenome indexing impractical and leaving some queries unanswered.
• What they did: The method replaces dense matrices for snarls above 500 children with hub labels built on a directed net-graph representation, using pruned landmark labeling ordered by contraction hierarchy.
• The result: Across four human chromosome pangenomes, the index uses an estimated 28x–119x less space for large snarls and supports 3–18.6% of node-to-node queries previously unanswerable, with build under 6 hours and under 50 GB.

AI summary of the abstract · may contain errors · not medical advice · read the paper.