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ntHash: recursive nucleotide hashing

Author:
Mohamadi, Hamid, Chu, Justin, Vandervalk, Benjamin P., Birol, Inanc
Source:
Bioinformatics 2016 v.32 no.22 pp. 3492-3494
ISSN:
1460-2059
Subject:
DNA, RNA, algorithms, bioinformatics, genome, nucleotide sequences, sequence alignment, transcriptome
Abstract:
Motivation: Hashing has been widely used for indexing, querying and rapid similarity search in many bioinformatics applications, including sequence alignment, genome and transcriptome assembly, k-mer counting and error correction. Hence, expediting hashing operations would have a substantial impact in the field, making bioinformatics applications faster and more efficient. Results: We present ntHash, a hashing algorithm tuned for processing DNA/RNA sequences. It performs the best when calculating hash values for adjacent k-mers in an input sequence, operating an order of magnitude faster than the best performing alternatives in typical use cases. Availability and implementation: ntHash is available online at http://www.bcgsc.ca/platform/bioinfo/software/nthash and is free for academic use. Contacts: hmohamadi@bcgsc.ca or ibirol@bcgsc.ca Supplementary information: Supplementary data are available at Bioinformatics online.
Agid:
6247483