Categories Link to heading ideas: 21 survey: 18 devops: 17 misc: 15 results: 11 method: 9 paper-review: 8 proposition: 6 thesis: 5 lablog: 4 walkthrough: 4 paper: 2 slides: 1 Tags Link to heading note: 23 pairwise-alignment: 18 highlight: 13 hpc: 13 minimizers: 12 linux: 11 astar: 9 suffix-array: 6 wayland: 6 data-structure: 5 mphf: 5 software: 5 wfa: 5 wip: 5 competitive-programming: 4 math: 4 teaching: 4 alignment: 3 binary-search: 3 genome-assembly: 3 nthash: 3 phylogeny: 3 conference-note...| CuriousCoding
Table of Contents Overview Detailed commentsGeneral Abstract 1. Introduction 2. Methods2.1 Outline 2.2 Indexing super-k-mers 2.3 Lazy encoding 2.4 Probing 2.5 Superbuckets 2.6 Implementation details 3. Results3.1 Parameters 3.2 Multicore 3.4 Comparison 3.5 Query times 4. Conclusion These are some (biased) comments on Brisk, a dynamic k-mer dictionary (Smith et al. 2024). Overview As is common these days, Brisk builds a dynamic k-mer dictionary using super-kmers, like e.g. SSHash (Pibiri 2022).| Posts on CuriousCoding
Table of Contents 1Introduction1.1Overview 1.2Previous reviews 2Theory of sampling schemes2.1Questions 2.2Types of schemes 2.3Parameter regimes 2.4Different perspectives 2.5UHS vs minimizer scheme 2.6(Asymptotic) bounds 2.7Lower bounds 3Minimizer schemes3.1Orders 3.2UHS-based and search-based schemes 3.3Pure schemes 3.4Other variantsSelection schemes Canonical minimizers 4Open questions 1 Introduction sadf Lots of DNA data Most algorithms deal with k-mers. k-mers overlap, and hence considerin...| Posts on CuriousCoding