RagnarGrootKoerkamp / simd-sketch
Compute bottom-s sketches and s-buckets sketches, using simd-minimizers crate.
☆16Updated last month
Alternatives and similar repositories for simd-sketch:
Users that are interested in simd-sketch are comparing it to the libraries listed below
- Iterate over minimizers of a DNA sequence☆28Updated 9 months ago
- Reference implementations of minimizer schemes to go with the mod-minimizers paper.☆24Updated last month
- Fast and exact gap-affine partial order alignment☆49Updated 2 weeks ago
- A SIMD-accelerated library to compute random minimizers☆16Updated 3 weeks ago
- Host depletion optimised for clinical metagenomic sequencing applications☆16Updated 5 months ago
- A Rust library providing fully dynamic sets of k-mers with high locality☆45Updated 6 months ago
- A FASTA/FASTQ format parser library☆20Updated last year
- Wavefront alignment algorithm (WFA) in Golang☆29Updated 5 months ago
- Compute a pairwise SNP distance matrix from one or two alignment(s)☆25Updated 7 months ago
- k-mers and the like☆21Updated this week
- COBS - Compact Bit-Sliced Signature Index (for Genomic k-Mer Data or q-Grams)☆19Updated 5 months ago
- A bit-packed k-mer representation (and relevant utilities) for rust☆48Updated 9 months ago
- Low level bindings and wrapper for slow5lib, an alternative for ONT Nanopore sequencing FAST5 output☆10Updated 5 months ago
- Dividing heterogeneous long-read sequencing into groups with de Bruijn graphs☆20Updated 5 months ago
- ☆14Updated 4 years ago
- Benchmarking pairwise aligners☆36Updated 2 months ago
- ☆13Updated 2 weeks ago
- A bioinformatics tool written in Rust to find palindromic sequences in DNA☆34Updated 2 months ago
- Shared k-mer content between two genomes☆17Updated last year
- Given a set of kmers (fasta format) and a set of sequences (fasta format), this tool will extract the sequences containing the kmers.☆21Updated last year
- Fulgor is a fast and space-efficient colored de Bruijn graph index.☆49Updated last week
- ☆12Updated 4 months ago
- Just another minhash implementation.☆12Updated last month
- HyLight is a strain aware de novo assembly method based on the overlap-layout-consensus (OLC) paradigm that leverages the strengths of NG…☆10Updated 7 months ago
- Contains the description of a file format to store kmers and associated values☆32Updated 2 years ago
- Drug Resistance Prediction with Reference Graphs☆20Updated last year
- ☆16Updated 2 months ago
- Rust package for constructing and analyzing phylogenies.☆15Updated 3 years ago
- HyGen: Compact and Efficient Genome Sketching using Hyperdimensional Vectors☆27Updated 8 months ago
- A Go implementation of the strobemers (https://github.com/ksahlin/strobemers)☆15Updated 4 years ago