Repository: Freie Universit├Ąt Berlin, Math Department

Raptor: A fast and space-efficient pre-filter for querying very large collections of nucleotide sequences

Seiler, Enrico and Mehringer, Svenja and Darvish, Mitra and Turc, Etienne and Reinert, Knut (2021) Raptor: A fast and space-efficient pre-filter for querying very large collections of nucleotide sequences. iScience, 24 (7). p. 102782. ISSN 25890042

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Official URL: https://doi.org/10.1016/j.isci.2021.102782

Abstract

We present Raptor, a tool for approximately searching many queries in large collections of nucleotide sequences. In comparison with similar tools like Mantis and COBS, Raptor is 12-144 times faster and uses up to 30 times less memory. Raptor uses winnowing minimizers to define a set of representative k-mers, an extension of the Interleaved Bloom Filters (IBF) as a set membership data structure, and probabilistic thresholding for minimizers. Our approach allows compression and a partitioning of the IBF to enable the effective use of secondary memory. Competing Interest Statement: The authors have declared no competing interest.

Item Type:Article
Subjects:Mathematical and Computer Sciences > Computer Science
Divisions:Department of Mathematics and Computer Science > Institute of Computer Science > Algorithmic Bioinformatics Group
ID Code:2519
Deposited By: Anja Kasseckert
Deposited On:18 Mar 2021 15:01
Last Modified:21 Sep 2021 13:20

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