will-rowe / genome-sketchingView external linksLinks
online notebooks for a review of genome sketching
☆60Sep 23, 2019Updated 6 years ago
Alternatives and similar repositories for genome-sketching
Users that are interested in genome-sketching are comparing it to the libraries listed below
Sorting:
- a toolset for fast DNA read set matching and assembly using a new type of reduced kmer☆37Aug 4, 2021Updated 4 years ago
- Histosketching Using Little Kmers☆56May 25, 2023Updated 2 years ago
- Generate kmers/minimizers/hashes/MinHash signatures, including with multiple kmer sizes.☆24Jan 9, 2021Updated 5 years ago
- A repository for generating strobemers and evalaution☆79Apr 16, 2024Updated last year
- Fast and accurate set similarity estimation via containment min hash☆42Jul 19, 2024Updated last year
- ProphAsm – a rapid computation of simplitigs directly from k-mer sets☆25Feb 17, 2023Updated 2 years ago
- ☆15Dec 8, 2022Updated 3 years ago
- Fast and precise comparison of genomes and metagenomes (in the order of terabytes) on a typical personal laptop☆72Jul 31, 2025Updated 6 months ago
- Classify sequencing reads using MinHash.☆48Apr 6, 2020Updated 5 years ago
- ☆24Apr 2, 2021Updated 4 years ago
- Space-efficient pseudoalignment with a colored de Bruijn graph☆52Mar 13, 2025Updated 11 months ago
- ☆30Sep 21, 2023Updated 2 years ago
- A database for signatures of public genomic sources☆18Jan 1, 2026Updated last month
- Dashing 2 is a fast toolkit for k-mer and minimizer encoding, sketching, comparison, and indexing.☆70Jun 17, 2024Updated last year
- A genomic minhashing implementation in Rust☆101Jun 17, 2025Updated 7 months ago
- Create Bloom filters for a given reference and then use it to categorize sequences☆76Nov 26, 2024Updated last year
- Iterate over minimizers of a DNA sequence☆31Jul 12, 2024Updated last year
- Wavefront alignment algorithm (WFA): Fast and exact gap-affine pairwise alignment☆199Mar 8, 2022Updated 3 years ago
- A resistome profiler for Graphing Resistance Out Of meTagenomes☆65May 11, 2020Updated 5 years ago
- Pan-genome inference and genotyping with long noisy or short accurate reads☆119Dec 13, 2024Updated last year
- Indel-aware consensus for aligned BAM☆21Aug 16, 2025Updated 6 months ago
- Contains the description of a file format to store kmers and associated values☆34Aug 17, 2022Updated 3 years ago
- FMSI is a highly memory efficient exact k-mer set index based on masked superstrings and the masked Burrows-Wheeler transform☆23Nov 20, 2025Updated 2 months ago
- An efficient index for the colored, compacted, de Bruijn graph☆111Oct 7, 2024Updated last year
- Kmer-db is a fast and memory-efficient tool for large-scale k-mer analyses (indexing, querying, estimating evolutionary relationships, et…☆97May 20, 2025Updated 8 months ago
- GFA insert into GenomicSQLite☆49Jun 7, 2021Updated 4 years ago
- compacted de Bruijn graph construction in low memory☆100Nov 4, 2025Updated 3 months ago
- A C++ library and utilities for manipulating the Graphical Fragment Assembly format.☆55May 17, 2022Updated 3 years ago
- modular k-mer count matrix and Bloom filter construction for large read collections☆86Dec 15, 2025Updated 2 months ago
- 📖 🧬 SSHash is a compressed, associative, exact, and weighted dictionary for k-mers.☆93Updated this week
- Peregrine: Fast Genome Assembler Using SHIMMER Index☆102Feb 6, 2022Updated 4 years ago
- Extracts subgraphs or components from a graph in GFA format☆24Nov 18, 2024Updated last year
- Mapping NCBI Genbank accession to GTDB accession☆14Feb 13, 2021Updated 5 years ago
- Minhash Index Extended to Knead Kmer Intersection☆11Mar 18, 2020Updated 5 years ago
- nimble aligner that will map your reads to the references on a laptop☆11Jun 29, 2017Updated 8 years ago
- A command line program for large scale buffering between piped programs☆16Nov 19, 2021Updated 4 years ago
- ☆62Sep 15, 2025Updated 5 months ago
- Transfer HiFi read mappings from their own assembly contigs to a standard reference☆29Dec 30, 2025Updated last month
- Embedding-based indexing for compact storage and rapid querying of bacterial pan-genomes☆21Dec 9, 2025Updated 2 months ago