ArticleBioinformatics (Oxford, England)2022
Sparse and skew hashing of K-mers.
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 39 papers.
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Who cites it
39 citing papers in PubMed.
- RSHash: a fast and space-efficient hash table for k-mers.Bioinformatics (Oxford, England) · 2026Article
- Optimizing sparse and skew hashing: faster k-mer dictionaries.Bioinformatics (Oxford, England) · 2026Article
- Hash functions in nucleotide sequence analysis.Genome research · 2026Review
- Optimizing sparse and skew hashing: fasterbioRxiv : the preprint server for biology · 2026Article
- Kaminari: a frugal colored index for approximateBioinformatics advances · 2026Article
- FroM Superstring to Indexing: a space-efficient index for unconstrainedBioinformatics advances · 2026Article
- genCRC32: collision-free CRC32-based hashing of DNA sequences.Bioinformatics advances · 2026Article
- Article
- Alevin-fry-atac enables rapid and memory frugal mapping of single-cell ATAC-seq data using virtual colors for accurate genomic pseudoalignment.Bioinformatics (Oxford, England) · 2025Article
- GreedyMini: generating low-density DNA minimizers.Bioinformatics (Oxford, England) · 2025Article
- The open-closed mod-minimizer algorithm.Algorithms for molecular biology : AMB · 2025Article
- MUSET: set of utilities for constructing abundance unitig matrices from sequencing data.Bioinformatics (Oxford, England) · 2025Article
- Fractional hitting sets for efficient multiset sketching.Algorithms for molecular biology : AMB · 2025Article
- K2R: Tinted de Bruijn graphs implementation for efficient read extraction from sequencing datasets.Bioinformatics advances · 2025Article
- A near-tight lower bound on the density of forward sampling schemes.Bioinformatics (Oxford, England) · 2024Article
- The backpack quotient filter: A dynamic and space-efficient data structure for queryingiScience · 2024Article
- A survey of k-mer methods and applications in bioinformatics.Computational and structural biotechnology journal · 2024Review
- kmerDB: A database encompassing the set of genomic and proteomic sequence information for each species.Computational and structural biotechnology journal · 2024Article
- A near-tight lower bound on the density of forward sampling schemes.bioRxiv : the preprint server for biology · 2024Article
- When less is more: sketching with minimizers in genomics.Genome biology · 2024Review
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1 author.
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No grant is acknowledged in the PubMed record.
Abstract
motivationA dictionary of k-mers is a data structure that stores a set of n distinct k-mers and supports membership queries. This data structure is at the hearth of many important tasks in computational biology. High-throughput sequencing of DNA can produce very large k-mer sets, in the size of billions of strings-in such cases, the memory consumption and query efficiency of the data structure is a concrete challenge.
resultsTo tackle this problem, we describe a compressed and associative dictionary for k-mers, that is: a data structure where strings are represented in compact form and each of them is associated to a unique integer identifier in the range [0,n). We show that some statistical properties of k-mer minimizers can be exploited by minimal perfect hashing to substantially improve the space/time trade-off of the dictionary compared to the best-known solutions. AVAILABILITY AND IMPLEMENTATION: https://github.com/jermp/sshash. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.