---
title: "biHash: bisulfite-aware rolling hashing for faster k-mer operations"
id: "biorxiv-5-bihash-bisulfite-aware-recursive-nucleotide-hashing"
canonical_url: "https://medichelpline.com/clinical-feed/biorxiv-5-bihash-bisulfite-aware-recursive-nucleotide-hashing"
content_type: "clinical_feed_article"
specialty: "General"
source_name: "bioRxiv (Biomedical Preprints)"
source_url: "https://www.biorxiv.org/content/10.64898/2026.10.19.760264v1?rss=1"
published_at: "2026-10-24T12:00:00.000Z"
evidence_level: "Verified Feed"
license: "CC-BY-NC-4.0 / Informational Use"
---
# biHash: bisulfite-aware rolling hashing for faster k-mer operations
## Provenance & Clinical Metadata
- **Canonical URL:** https://medichelpline.com/clinical-feed/biorxiv-5-bihash-bisulfite-aware-recursive-nucleotide-hashing
- **Specialty:** [General](https://medichelpline.com/clinical-feed/general.md)
- **Primary Source:** bioRxiv (Biomedical Preprints)
- **Source URL:** [Original Journal Publication](https://www.biorxiv.org/content/10.64898/2026.10.19.760264v1?rss=1)
- **Published At:** 2026-10-24T12:00:00.000Z
- **Evidence Rating:** Verified Feed
## Executive GIST (TL;DR)
- The preprint introduces **biHash**, a rolling hash algorithm specifically designed for **bisulfite sequencing** data and its reduced-complexity alphabet. - Bisulfite conversion changes unmethylated cytosines to thymines, which disrupts strand complementarity and lowers sequence complexity; the authors framed this as a challenge for conventional hashing. - biHash uses context-specific dinucleotide encodings to map bisulfite-compatible sequence variants to the same hash value while preserving context-specific specificity. - The algorithm operates as a rolling hash, enabling rapid computation when moving between adjacent **k-mer** windows. - When hashing adjacent **k-mer** sequences, the study team observed biHash performed approximately 13 times faster than generic string hashing algorithms. - The authors positioned biHash as a solution to enable more efficient sequence comparison and indexing tasks for bisulfite-treated reads. - The source did not report implementation details such as exact encoding tables, memory usage, or benchmarking dataset composition in this abstract; those details may be in the full text or supplementary material. - The preprint is not yet peer reviewed; authors declared no competing interests and acknowledged NSERC support.
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These pose a fundamental challenge to efficient sequence comparison and indexing tasks. Although _k_ -mer hashing is foundational to bioinformatics for enabling such high-throughput operations, generic algorithms for string hashing are poorly equipped to handle the reduced-complexity alphabet and sequence ambiguity created by this conversion. We therefore require fast _k_ -mer hashing that directly recognizes bisulfite-compatible sequence states. Here, we present biHash, a rolling hash algorithm tailored for bisulfite-sequenced data. Using context-specific dinucleotide encodings, biHash maps designated bisulfite-compatible sequence variants to the same hash value while retaining context-specific specificity. When hashing adjacent _k_ -mers, biHash performs ~13 times faster than generic string hashing algorithms. ### Competing Interest Statement The authors have declared no competing interest. ## Funder Information Declared Natural Sciences and Engineering Research Council of Canada, CGS D - 589478  2024 Copyright The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a [CC-BY-NC 4.0 International license](http://creativecommons.org/licenses/by-nc/4.0/). bioRxiv and medRxiv thank the following for their generous financial support: > The Chan Zuckerberg Initiative, Cold Spring Harbor Laboratory, the Sergey Brin Family Foundation, California Institute of Technology, Centre National de la Recherche Scientifique, Fred Hutchinson Cancer Center, Imperial College London, Massachusetts Institute of Technology, Stanford University, The University of Edinburgh, University of Washington, and Vrije Universiteit Amsterdam. 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[ Download PDF](https://www.biorxiv.org/content/10.64898/2026.10.19.760264v1.full.pdf) Print/Save Options [Download PDF](https://www.biorxiv.org/content/biorxiv/early/2026/10/24/2026.10.19.760264.full.pdf)Full Text & In-line FiguresXML [More Info](https://www.biorxiv.org/about/FAQ#PrintOptions "More Information on Print/Save Options") [Supplementary Material ](https://www.biorxiv.org/content/10.64898/2026.10.19.760264v1.supplementary-material) [ Email](https://www.biorxiv.org/ "Email this Article") [ Share](https://www.biorxiv.org/) biHash: bisulfite-aware recursive nucleotide hashing johnathan wong, Inanc Birol bioRxiv 2026.10.19.760264; doi: https://doi.org/10.64898/2026.10.19.760264 This article is a preprint and has not been certified by peer review [[what does this mean?](https://www.biorxiv.org/about/FAQ#unrefereed)]. 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