Genome Biology (May 2023)

Hierarchical Interleaved Bloom Filter: enabling ultrafast, approximate sequence queries

  • Svenja Mehringer,
  • Enrico Seiler,
  • Felix Droop,
  • Mitra Darvish,
  • René Rahn,
  • Martin Vingron,
  • Knut Reinert

DOI
https://doi.org/10.1186/s13059-023-02971-4
Journal volume & issue
Vol. 24, no. 1
pp. 1 – 25

Abstract

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Abstract We present a novel data structure for searching sequences in large databases: the Hierarchical Interleaved Bloom Filter (HIBF). It is extremely fast and space efficient, yet so general that it could serve as the underlying engine for many applications. We show that the HIBF is superior in build time, index size, and search time while achieving a comparable or better accuracy compared to other state-of-the-art tools. The HIBF builds an index up to 211 times faster, using up to 14 times less space, and can answer approximate membership queries faster by a factor of up to 129.

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