ArticlebioRxiv : the preprint server for biology2026
Optimizing sparse and skew hashing: faster
Article in bioRxiv : the preprint server for biology, 2026. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Not yet cited in PubMed.
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Abstract
Motivation: Representing a set of Results: We study the problem of accelerating queries under the sparse and skew hashing indexing paradigm, without compromising its space effectiveness. We propose a refined data structure with less complex lookups and fewer cache misses. We give a simpler and faster algorithm for streaming lookup queries. Compared to indexes with similar capabilities and based on the Burrows-Wheeler transform, like SBWT and FMSI, SSHash is significantly faster to build and query. SSHash is competitive in space with the fast (and default) modality of SBWT when both Availability and Implementation: The SSHash software is available at https://github.com/jermp/sshash, and also distributed via Bioconda. A benchmark of data structures for Contact: giulioermanno.pibiri@unive.it, rob@cs.umd.edu.
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