Chopper

Abstract

Chopper uses a hierarchical DP algorithm to pack user bins into a given number technical bins, optimizing the space consumption of a Hierarchical Binning Directory.

Links

• Official Website
• View the source code and README on GitHub

Please Cite

• Svenja Mehringer, Enrico Seiler, Felix Droop, Mitra Darvish, René Rahn, Martin Vingron, Knut Reinert, “Hierarchical Interleaved Bloom Filter: enabling ultrafast, approximate sequence queries”, vol. 24, iss. 131, 2023-05-31.
  cite this publication

  @article{fu_mi_publications2846,
   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. 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 (Mantis
    and Bifrost). 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. This can be considered
    a quantum leap that opens the door to indexing complete sequence archives like the European
    Nucleotide Archive or even larger metagenomics data sets.},
   author = {Svenja Mehringer and Enrico Seiler and Felix Droop and Mitra Darvish and Ren{\'e} Rahn
    and Martin Vingron and Knut Reinert},
   booktitle = {Hierarchical Interleaved Bloom Filter: Enabling ultrafast, approximate sequence
    queries},
   journal = {Genome Biology},
   month = {May},
   number = {131},
   publisher = {BioMed Central},
   title = {Hierarchical Interleaved Bloom Filter: enabling ultrafast, approximate sequence queries},
   url = {http://publications.imp.fu-berlin.de/2846/},
   volume = {24},
   year = {2023}
  }

Contact

For questions, comments, or suggestions please contact:

Svenja Mehringer