{"paper":{"title":"cuSBF: A Minimizer-Aware Bloom Filter for Genomic Sequence Data on Modern GPUs","license":"http://creativecommons.org/licenses/by/4.0/","headline":"","cross_cats":["cs.DS","q-bio.GN"],"primary_cat":"cs.DC","authors_text":"Bertil Schmidt, Markus Vieth, Tim Dortmann","submitted_at":"2026-06-23T10:53:34Z","abstract_excerpt":"Efficient genomic k-mer indexing depends on approximate membership query (AMQ) structures that must deliver high throughput, low false-positive rates (FPR), and modest memory footprints. The Super Bloom filter (SBF) is attractive for this scenario because minimizer-guided sharding and the Findere scheme exploit the redundancy of overlapping k-mers. However, those same features cause high per-k-mer compute cost, severe register pressure, and irregular memory accesses, which hinder an effective GPU implementation. We present cuSBF, an open-source, header-only CUDA library that implements SBF for"},"claims":{"count":0,"items":[],"snapshot_sha256":"258153158e38e3291e3d48162225fcdb2d5a3ed65a07baac614ab91432fd4f57"},"source":{"id":"2606.24417","kind":"arxiv","version":1},"verdict":{"id":null,"model_set":{},"created_at":null,"strongest_claim":"","one_line_summary":"","pipeline_version":null,"weakest_assumption":"","pith_extraction_headline":""},"integrity":{"clean":true,"summary":{"advisory":0,"critical":0,"by_detector":{},"informational":0},"endpoint":"/pith/2606.24417/integrity.json","findings":[],"available":true,"detectors_run":[],"snapshot_sha256":"c28c3603d3b5d939e8dc4c7e95fa8dfce3d595e45f758748cecf8e644a296938"},"references":{"count":0,"sample":[],"resolved_work":0,"snapshot_sha256":"258153158e38e3291e3d48162225fcdb2d5a3ed65a07baac614ab91432fd4f57","internal_anchors":0},"formal_canon":{"evidence_count":0,"snapshot_sha256":"258153158e38e3291e3d48162225fcdb2d5a3ed65a07baac614ab91432fd4f57"},"author_claims":{"count":0,"strong_count":0,"snapshot_sha256":"258153158e38e3291e3d48162225fcdb2d5a3ed65a07baac614ab91432fd4f57"},"builder_version":"pith-number-builder-2026-05-17-v1"}