Dataset Information
NtHash: recursive nucleotide hashing.
Ontology highlight
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.caSupplementary information: Supplementary data are available at Bioinformatics online.
SUBMITTER: Mohamadi H
PROVIDER: S-EPMC5181554 | biostudies-literature | 2016 Nov
REPOSITORIES: biostudies-literature
Publications
ntHash: recursive nucleotide hashing.
Bioinformatics (Oxford, England) 20160716 22
<h4>Motivation</h4>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.<h4>Results</h4>We present ntHash, a hashing algorithm tuned for processing DNA/RNA sequences. It performs the best wh ...[more]