RagnarGrootKoerkamp / simd-sketch
Compute bottom-s sketches and s-buckets sketches, using simd-minimizers crate.
☆16Updated 2 weeks ago
Alternatives and similar repositories for simd-sketch:
Users that are interested in simd-sketch are comparing it to the libraries listed below
- Fast and exact gap-affine partial order alignment☆49Updated 4 months ago
- Iterate over minimizers of a DNA sequence☆28Updated 8 months ago
- A SIMD-accelerated library to compute random minimizers☆14Updated this week
- A Rust library providing fully dynamic sets of k-mers with high locality☆44Updated 6 months ago
- Reference implementations of minimizer schemes to go with the mod-minimizers paper.☆24Updated 3 weeks ago
- Wavefront alignment algorithm (WFA) in Golang☆29Updated 5 months ago
- k-mers and the like☆21Updated last week
- Compute a pairwise SNP distance matrix from one or two alignment(s)☆24Updated 6 months ago
- Bioinformatics 101 tool for counting unique k-length substrings in DNA☆30Updated last year
- A FASTA/FASTQ format parser library☆20Updated last year
- Rust library for processing sequencing reads.☆21Updated 6 months ago
- ☆13Updated 2 weeks ago
- Dividing heterogeneous long-read sequencing into groups with de Bruijn graphs☆20Updated 4 months ago
- Host depletion optimised for clinical metagenomic sequencing applications☆15Updated 4 months ago
- Fulgor is a fast and space-efficient colored de Bruijn graph index.☆49Updated last month
- COBS - Compact Bit-Sliced Signature Index (for Genomic k-Mer Data or q-Grams)☆18Updated 4 months ago
- Experiments with using BIGSI data structure for metagenomic and QC applications☆19Updated 7 months ago
- Just another minhash implementation.☆12Updated last month
- ☆12Updated 3 months ago
- A long read simulator based on badread idea☆22Updated 2 years ago
- Shared k-mer content between two genomes☆17Updated last year
- A bit-packed k-mer representation (and relevant utilities) for rust☆48Updated 9 months ago
- Rust package for constructing and analyzing phylogenies.☆15Updated 3 years ago
- Low level bindings and wrapper for slow5lib, an alternative for ONT Nanopore sequencing FAST5 output☆10Updated 4 months ago
- HyGen: Compact and Efficient Genome Sketching using Hyperdimensional Vectors☆26Updated 7 months ago
- Generate random test data for bioinformatics☆26Updated 9 months ago
- ☆16Updated last month
- Remove human reads from a sequencing run☆38Updated 6 months ago
- A bioinformatics tool written in Rust to find palindromic sequences in DNA☆34Updated 2 months ago
- fast, multithreaded sourmash operations: search, compare, and gather.☆22Updated this week