ArticleBioinformatics (Oxford, England)2022
Theory of local k-mer selection with applications to long-read alignment.
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 34 papers.
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34 citing papers in PubMed.
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- Efficient De Novo Assembly and Recovery of Microbial Genomes from Complex Metagenomes Using a Reduced Set of k-mers.Interdisciplinary sciences, computational life sciences · 2026Article
- Elucidating Transitions ofJournal of computational biology : a journal of computational molecular cell biology · 2026Article
- Density-reducing Jaccard estimators for sketch-based long read applications.BMC bioinformatics · 2025Article
- High-resolution metagenome assembly for modern long reads with myloasm.bioRxiv : the preprint server for biology · 2025Article
- Genomic language models with k-mer tokenization strategies for plant genome annotation and regulatory element strength prediction.Plant molecular biology · 2025Article
- The open-closed mod-minimizer algorithm.Algorithms for molecular biology : AMB · 2025Article
- A near-tight lower bound on the density of forward sampling schemes.Bioinformatics (Oxford, England) · 2024Article
- The Statistics of Parametrized Syncmers in a Simple Mutation Process Without Spurious Matches.Journal of computational biology : a journal of computational molecular cell biology · 2024Article
- A near-tight lower bound on the density of forward sampling schemes.bioRxiv : the preprint server for biology · 2024Article
- k-nonical space: sketching with reverse complements.Bioinformatics (Oxford, England) · 2024Article
- Fast and space-efficient taxonomic classification of long reads with hierarchical interleaved XOR filters.Genome research · 2024Article
- Sketching Methods with Small Window Guarantee Using Minimum Decycling Sets.Journal of computational biology : a journal of computational molecular cell biology · 2024Article
- Application and Comparison of Machine Learning and Database-Based Methods in Taxonomic Classification of High-Throughput Sequencing Data.Genome biology and evolution · 2024Article
- Density and Conservation Optimization of the Generalized Masked-Minimizer Sketching Scheme.Journal of computational biology : a journal of computational molecular cell biology · 2024Article
- Screening Host Genomic Data for Wolbachia Infections.Methods in molecular biology (Clifton, N.J.) · 2024Article
- Creating and Using Minimizer Sketches in Computational Genomics.Journal of computational biology : a journal of computational molecular cell biology · 2023Review
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Abstract
motivationSelecting a subset of k-mers in a string in a local manner is a common task in bioinformatics tools for speeding up computation. Arguably the most well-known and common method is the minimizer technique, which selects the 'lowest-ordered' k-mer in a sliding window. Recently, it has been shown that minimizers may be a sub-optimal method for selecting subsets of k-mers when mutations are present. There is, however, a lack of understanding behind the theory of why certain methods perform well.
resultsWe first theoretically investigate the conservation metric for k-mer selection methods. We derive an exact expression for calculating the conservation of a k-mer selection method. This turns out to be tractable enough for us to prove closed-form expressions for a variety of methods, including (open and closed) syncmers, (a, b, n)-words, and an upper bound for minimizers. As a demonstration of our results, we modified the minimap2 read aligner to use a more conserved k-mer selection method and demonstrate that there is up to an 8.2% relative increase in number of mapped reads. However, we found that the k-mers selected by more conserved methods are also more repetitive, leading to a runtime increase during alignment. We give new insight into how one might use new k-mer selection methods as a reparameterization to optimize for speed and alignment quality. AVAILABILITY AND IMPLEMENTATION: Simulations and supplementary methods are available at https://github.com/bluenote-1577/local-kmer-selection-results. os-minimap2 is a modified version of minimap2 and available at https://github.com/bluenote-1577/os-minimap2. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
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