ArticleBioinformatics (Oxford, England)2022
ntHash2: recursive spaced seed hashing for nucleotide sequences.
Article in Bioinformatics (Oxford, England), 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 10 papers.
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Who cites it
10 citing papers in PubMed.
- Hash functions in nucleotide sequence analysis.Genome research · 2026Review
- Genome misassembly detection using Stash: A data structure based on stochastic tile hashing.PloS one · 2026Article
- ntSynt: multi-genome synteny detection using minimizer graph mappings.BMC biology · 2025Article
- Fast and flexible minimizer digestion with digest.Bioinformatics (Oxford, England) · 2025Article
- Taming large-scale genomic analyses via sparsified genomics.Nature communications · 2025Article
- kmerDB: A database encompassing the set of genomic and proteomic sequence information for each species.Computational and structural biotechnology journal · 2024Article
- Linear time complexity de novo long read genome assembly with GoldRush.Nature communications · 2023Article
- ntLink: A Toolkit for De Novo Genome Assembly Scaffolding and Mapping Using Long Reads.Current protocols · 2023Article
- aaHash: recursive amino acid sequence hashing.Bioinformatics advances · 2023Article
- Comparison of k-mer-basedMicrobiome research reports · 2023Article
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6 authors.
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Abstract
motivationSpaced seeds are robust alternatives to k-mers in analyzing nucleotide sequences with high base mismatch rates. Hashing is also crucial for efficiently storing abundant sequence data. Here, we introduce ntHash2, a fast algorithm for spaced seed hashing that can be integrated into various bioinformatics tools for efficient sequence analysis with applications in genome research.
resultsntHash2 is up to 2.1× faster at hashing various spaced seeds than the previous version and 3.8× faster than conventional hashing algorithms with naïve adaptation. Additionally, we reduced the collision rate of ntHash for longer k-mer lengths and improved the uniformity of the hash distribution by modifying the canonical hashing mechanism. AVAILABILITY AND IMPLEMENTATION: ntHash2 is freely available online at github.com/bcgsc/ntHash under an MIT license. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
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