RagnarGrootKoerkamp / simd-sketchLinks
Compute bottom-s sketches and s-buckets sketches, using simd-minimizers crate.
☆17Updated last week
Alternatives and similar repositories for simd-sketch
Users that are interested in simd-sketch are comparing it to the libraries listed below
Sorting:
- k-mers and the like☆22Updated last week
- Iterate over minimizers of a DNA sequence☆30Updated 11 months ago
- Fast and exact gap-affine partial order alignment☆51Updated 2 weeks ago
- A SIMD-accelerated library to compute random minimizers☆29Updated last week
- Host depletion optimised for clinical metagenomic sequencing applications☆16Updated 7 months ago
- Fast sequence distance estimates☆11Updated 2 weeks ago
- Reference implementations of minimizer schemes to go with the mod-minimizers paper.☆25Updated 2 months ago
- Compute a pairwise SNP distance matrix from one or two alignment(s)☆25Updated 9 months ago
- A FASTA/FASTQ format parser library☆20Updated last year
- A Rust library providing fully dynamic sets of k-mers with high locality☆45Updated 8 months ago
- Bioinformatics 101 tool for counting unique k-length substrings in DNA☆31Updated last year
- Dividing heterogeneous long-read sequencing into groups with de Bruijn graphs☆25Updated 7 months ago
- Just another minhash implementation.☆12Updated 3 weeks ago
- COBS - Compact Bit-Sliced Signature Index (for Genomic k-Mer Data or q-Grams)☆20Updated 7 months ago
- A minimap2 implementation with binseq inputs☆14Updated last month
- ☆12Updated 6 months ago
- ☆13Updated 2 months ago
- A "Navie" Implementation of the Wavefront Algorithm For Sequence Alignment with Gap-Affine Scoring☆15Updated last year
- ☆17Updated 4 months ago
- Wavefront alignment algorithm (WFA) in Golang☆29Updated 7 months ago
- Fast (host) DNA sequence filtering☆60Updated this week
- Sketch-based surveillance platform☆13Updated 6 months ago
- Shared k-mer content between two genomes☆18Updated 2 years ago
- Optimal sequence-to-graph alignment with recombinations☆32Updated 4 months ago
- De novo metagenome assembler☆13Updated 2 years ago
- FMSI is a highly memory efficient exact k-mer set index based on masked superstrings and the masked Burrows-Wheeler transform☆20Updated 5 months ago
- 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
- GBWT in Rust☆43Updated 2 months ago
- A bioinformatics tool written in Rust to find palindromic sequences in DNA☆35Updated 4 months ago
- Low level bindings and wrapper for slow5lib, an alternative for ONT Nanopore sequencing FAST5 output☆10Updated 7 months ago