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

[email protected] or [email protected]

Supplementary information

Supplementary data are available at Bioinformatics online.

© The Author 2016. Published by Oxford University Press.
2016
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