Kmer-db is a fast and memory-efficient tool for large-scale k-mer analyses (indexing, querying, estimating evolutionary relationships, etc.).
☆97May 20, 2025Updated 10 months ago
Alternatives and similar repositories for kmer-db
Users that are interested in kmer-db are comparing it to the libraries listed below. We may earn a commission when you buy through links labeled 'Ad' on this page.
Sorting:
- Fast and frugal disk based k-mer counter☆327Mar 10, 2026Updated 2 weeks ago
- fast, multithreaded sourmash operations: search, compare, and gather.☆25Mar 16, 2026Updated last week
- Accurate and fast taxonomic classification using pseudoaligning☆21Sep 16, 2017Updated 8 years ago
- Classify sequencing reads using MinHash.☆48Apr 6, 2020Updated 5 years ago
- Fast and accurate set similarity estimation via containment min hash☆42Jul 19, 2024Updated last year
- RabbitMash: an efficient highly optimized implementation of Mash.☆20Oct 28, 2023Updated 2 years ago
- Histosketching Using Little Kmers☆57May 25, 2023Updated 2 years ago
- Generate kmers/minimizers/hashes/MinHash signatures, including with multiple kmer sizes.☆24Jan 9, 2021Updated 5 years ago
- A fast and space-efficient pre-filter for querying very large collections of nucleotide sequences.☆53Updated this week
- Fast and precise comparison of genomes and metagenomes (in the order of terabytes) on a typical personal laptop☆74Jul 31, 2025Updated 7 months ago
- Reference-free variant discovery in large eukaryotic genomes☆42Jul 13, 2021Updated 4 years ago
- kProcessor: kmers processing framework.☆10Oct 1, 2023Updated 2 years ago
- A versatile toolkit for k-mers with taxonomic information☆82Aug 28, 2025Updated 6 months ago
- ☆15Jan 28, 2026Updated last month
- ProphAsm – a rapid computation of simplitigs directly from k-mer sets☆25Feb 17, 2023Updated 3 years ago
- Computation of average nucleotide identity with the use of MMseqs2☆16Dec 11, 2024Updated last year
- Building the compacted de Bruijn graph efficiently from references or reads.☆92Feb 26, 2026Updated 3 weeks ago
- ☆286Dec 29, 2025Updated 2 months ago
- ☆26Aug 10, 2021Updated 4 years ago
- BItsliced Genomic Signature Index - Efficient indexing and search in very large collections of WGS data☆124Aug 24, 2023Updated 2 years ago
- REINDEER REad Index for abuNDancE quERy☆56Jul 6, 2025Updated 8 months ago
- Ococo: the first online variant and consensus caller. Call genomic consensus directly from an unsorted SAM/BAM stream.☆46Jan 18, 2019Updated 7 years ago
- Metagenomic profiling and phylogenetic distances via common kmers☆42Jul 12, 2021Updated 4 years ago
- Next Index to Query Kmer Intersection☆17Feb 1, 2023Updated 3 years ago
- A genomic minhashing implementation in Rust☆103Jun 17, 2025Updated 9 months ago
- Hybrid error correction of long reads using colored de Bruijn graphs☆108Jan 17, 2026Updated 2 months ago
- Split Kmer Analysis☆66May 26, 2022Updated 3 years ago
- Genome inference from a population reference graph☆96Apr 1, 2025Updated 11 months ago
- Fast and accurate genomic distances using HyperLogLog☆163Jan 19, 2023Updated 3 years ago
- Mantis: A Fast, Small, and Exact Large-Scale Sequence-Search Index☆86Mar 7, 2024Updated 2 years ago
- Simka and SimkaMin are comparative metagenomics methods dedicated to NGS datasets.☆51Feb 8, 2022Updated 4 years ago
- a toolset for fast DNA read set matching and assembly using a new type of reduced kmer☆37Aug 4, 2021Updated 4 years ago
- Space-efficient pseudoalignment with a colored de Bruijn graph☆52Mar 13, 2025Updated last year
- SeqOthello supports fast coverage query and containment query.☆12May 8, 2019Updated 6 years ago
- Pangenome graphs (review article on graph-based pangenomic methods)☆72Apr 15, 2020Updated 5 years ago
- Accurate metagenomic profiling && Fast large-scale sequence/genome searching☆208Sep 22, 2023Updated 2 years ago
- kaamer - protein identification based on amino acid kmers☆12Mar 7, 2023Updated 3 years ago
- Graph-based assembly phasing☆91Nov 25, 2025Updated 3 months ago
- CAMITAX: Taxon labels for microbial genomes☆31Dec 14, 2023Updated 2 years ago