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COBS: A Compact Bit-Sliced Signature Index

  • Timo BingmannEmail author
  • Phelim Bradley
  • Florian Gauger
  • Zamin Iqbal
Conference paper
Part of the Lecture Notes in Computer Science book series (LNCS, volume 11811)

Abstract

We present COBS, a COmpact Bit-sliced Signature index, which is a cross-over between an inverted index and Bloom filters. Our target application is to index k-mers of DNA samples or q-grams from text documents and process approximate pattern matching queries on the corpus with a user-chosen coverage threshold. Query results may contain a number of false positives which decreases exponentially with the query length. We compare COBS to seven other index software packages on 100 000 microbial DNA samples. COBS’ compact but simple data structure outperforms the other indexes in construction time and query performance with Mantis by Pandey et al. in second place. However, unlike Mantis and other previous work, COBS does not need the complete index in RAM and is thus designed to scale to larger document sets.

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Copyright information

© Springer Nature Switzerland AG 2019

Authors and Affiliations

  • Timo Bingmann
    • 1
    Email author
  • Phelim Bradley
    • 2
  • Florian Gauger
    • 1
  • Zamin Iqbal
    • 2
  1. 1.Institute of Theoretical InformaticsKarlsruhe Institute of TechnologyKarlsruheGermany
  2. 2.European Molecular Biology LaboratoryEuropean Bioinformatics InstituteCambridgeUK

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