π 𧬠SSHash is a compressed, associative, exact, and weighted dictionary for k-mers.
β94Mar 17, 2026Updated this week
Alternatives and similar repositories for sshash
Users that are interested in sshash are comparing it to the libraries listed below
Sorting:
- Fast and compact locality-preserving minimal perfect hashing for k-mer sets.β44Nov 18, 2023Updated 2 years ago
- Space-efficient pseudoalignment with a colored de Bruijn graphβ52Mar 13, 2025Updated last year
- A small, auxiliary index to massively improve parallel fastq parsingβ31Mar 6, 2026Updated 2 weeks ago
- ProphAsm β a rapid computation of simplitigs directly from k-mer setsβ25Feb 17, 2023Updated 3 years ago
- Next Index to Query Kmer Intersectionβ17Feb 1, 2023Updated 3 years ago
- β‘οΈ π§¬ Fulgor is a fast and space-efficient colored de Bruijn graph index.β60Updated this week
- a toolset for fast DNA read set matching and assembly using a new type of reduced kmerβ37Aug 4, 2021Updated 4 years ago
- A repository for generating strobemers and evalautionβ79Apr 16, 2024Updated last year
- A SIMD-accelerated library to compute random minimizersβ39Mar 1, 2026Updated 2 weeks ago
- Contains the description of a file format to store kmers and associated valuesβ34Aug 17, 2022Updated 3 years ago
- Compacted and colored de Bruijn graph construction and queryingβ94Mar 6, 2026Updated 2 weeks ago
- Fast approximate string searchingβ114Updated this week
- A Rust library providing fully dynamic sets of k-mers with high localityβ47Feb 12, 2026Updated last month
- FMSI is a highly memory efficient exact k-mer set index based on masked superstrings and the masked Burrows-Wheeler transformβ24Nov 20, 2025Updated 4 months ago
- Fast, Cache-Efficient, and Scalable Queries on Pangenomesβ38Mar 9, 2026Updated last week
- A reimplementation of the WaveFront Alignment algorithm at low memoryβ50May 22, 2024Updated last year
- Iterate over minimizers of a DNA sequenceβ32Jul 12, 2024Updated last year
- nimble aligner that will map your reads to the references on a laptopβ11Jun 29, 2017Updated 8 years ago
- Classify sequencing reads using MinHash.β48Apr 6, 2020Updated 5 years ago
- KmerCamelπ« provides implementations of several algorithms for efficiently representing a set of k-mers as a masked superstring.β20Sep 13, 2025Updated 6 months ago
- Dashing 2 is a fast toolkit for k-mer and minimizer encoding, sketching, comparison, and indexing.β70Jun 17, 2024Updated last year
- Iterate k-min-mers from a DNA sequence in Rustβ13Apr 8, 2024Updated last year
- β21Dec 26, 2025Updated 2 months ago
- Minimum plain text representation of kmer setsβ16Jan 30, 2025Updated last year
- compacted de Bruijn graph construction in low memoryβ100Nov 4, 2025Updated 4 months ago
- Robust individual and aggregate checksums for nucleotide sequencesβ17Mar 3, 2026Updated 2 weeks ago
- Pan-genome inference and genotyping with long noisy or short accurate readsβ119Dec 13, 2024Updated last year
- De Bruijn graph representation in low memoryβ35Jul 6, 2024Updated last year
- βοΈ PTHash is a fast and compact minimal perfect hash function.β252Mar 9, 2026Updated last week
- modular k-mer count matrix and Bloom filter construction for large read collectionsβ86Dec 15, 2025Updated 3 months ago
- β28Sep 28, 2024Updated last year
- Pan-Genomic Matching Statisticsβ55Apr 3, 2024Updated last year
- Generate kmers/minimizers/hashes/MinHash signatures, including with multiple kmer sizes.β24Jan 9, 2021Updated 5 years ago
- Optimal distance lower bound k-mer sampling.β12Jun 19, 2024Updated last year
- Fast and Memory Efficient Genome Sketching via HyperLogLog, HyperMinHash and UltraLogLogβ20Jan 22, 2026Updated last month
- β24Apr 2, 2021Updated 4 years ago
- REINDEER REad Index for abuNDancE quERyβ56Jul 6, 2025Updated 8 months ago
- Fast FASTA/Q parser and writer (C++ re-implementation of kseq library)β57Mar 4, 2024Updated 2 years ago
- Building the compacted de Bruijn graph efficiently from references or reads.β92Feb 26, 2026Updated 3 weeks ago