Index kmtricks bf matrices
☆47Feb 13, 2026Updated last month
Alternatives and similar repositories for kmindex
Users that are interested in kmindex are comparing it to the libraries listed below
Sorting:
- modular k-mer count matrix and Bloom filter construction for large read collections☆86Dec 15, 2025Updated 3 months ago
- ProphAsm – a rapid computation of simplitigs directly from k-mer sets☆25Feb 17, 2023Updated 3 years ago
- Iterate over minimizers of a DNA sequence☆32Jul 12, 2024Updated last year
- Space-efficient pseudoalignment with a colored de Bruijn graph☆52Mar 13, 2025Updated last year
- Minimum plain text representation of kmer sets☆16Jan 30, 2025Updated last year
- Differential k-mer analysis☆40Jan 29, 2024Updated 2 years ago
- Implementation of a Backpack Quotient Filter☆13Jul 7, 2025Updated 8 months ago
- Approximate nearest neighbour search for microbial genomes based on hash metric☆62Mar 7, 2026Updated 2 weeks ago
- ☆16Jun 22, 2023Updated 2 years ago
- Given a set of kmers (fasta format) and a set of sequences (fasta format), this tool will extract the sequences containing the kmers.☆21Oct 20, 2023Updated 2 years ago
- Embedding-based indexing for compact storage and rapid querying of bacterial pan-genomes☆21Dec 9, 2025Updated 3 months ago
- Rapid estimation of phylogenetic trees using sketching☆13Feb 18, 2025Updated last year
- Compacted and colored de Bruijn graph construction and querying☆94Mar 6, 2026Updated 2 weeks ago
- compacted de Bruijn graph construction in low memory☆100Nov 4, 2025Updated 4 months ago
- Building the compacted de Bruijn graph efficiently from references or reads.☆92Feb 26, 2026Updated 3 weeks ago
- Contains the description of a file format to store kmers and associated values☆34Aug 17, 2022Updated 3 years ago
- A database for signatures of public genomic sources☆18Jan 1, 2026Updated 2 months ago
- Fast and compact locality-preserving minimal perfect hashing for k-mer sets.☆44Nov 18, 2023Updated 2 years ago
- Computation of average nucleotide identity with the use of MMseqs2☆16Dec 11, 2024Updated last year
- Phylogenetic compression of extremely large genome collections [661k ↘𝟭𝟲𝗚𝗶𝗕 | BIGSIdata ↘𝟰𝟴𝗚𝗶𝗕 | AllTheBact'23 ↘𝟳𝟱𝗚𝗶𝗕]☆47Apr 1, 2025Updated 11 months ago
- Scalable annotated de Bruijn graphs for DNA indexing, alignment, and assembly☆223Updated this week
- Bifrost graph gene caller.☆98Jan 20, 2026Updated 2 months ago
- A "Navie" Implementation of the Wavefront Algorithm For Sequence Alignment with Gap-Affine Scoring☆14Aug 7, 2023Updated 2 years ago
- Host depletion optimised for clinical metagenomic sequencing applications☆16Nov 18, 2024Updated last year
- Alignment against all pre-2019 bacteria on laptops within a few hours (former MOF-Search)☆41Apr 17, 2024Updated last year
- sunburst plots for taxonomy - working to update Krona☆44Sep 22, 2025Updated 5 months ago
- Fast, Cache-Efficient, and Scalable Queries on Pangenomes☆38Mar 9, 2026Updated last week
- A fast constructor of the compressed de Bruijn graph from many genomes☆42Nov 27, 2025Updated 3 months ago
- Accurate, resource-frugal and deterministic DNA sequence classifier.☆36Mar 4, 2026Updated 2 weeks ago
- FMSI is a highly memory efficient exact k-mer set index based on masked superstrings and the masked Burrows-Wheeler transform☆24Nov 20, 2025Updated 4 months ago
- A SIMD-accelerated library to compute random minimizers☆39Mar 1, 2026Updated 2 weeks ago
- MetagenOmic read Re-Assigner and abundance quantifier☆20Jan 31, 2025Updated last year
- Fast Scalable Minimal Perfect Hash for Large Keysets☆32Feb 8, 2025Updated last year
- REINDEER REad Index for abuNDancE quERy☆56Jul 6, 2025Updated 8 months ago
- A k-mer search engine for all Sequence Read Archive public accessions☆37Oct 29, 2024Updated last year
- ⚡️ 🧬 Fulgor is a fast and space-efficient colored de Bruijn graph index.☆60Updated this week
- A Rust library providing fully dynamic sets of k-mers with high locality☆47Feb 12, 2026Updated last month
- Orpheum (Previously called and published under sencha) is a Python package for directly translating RNA-seq reads into coding protein seq…☆19Oct 4, 2022Updated 3 years ago
- SIMD-parallel BLAST X-drop DP on sequence graphs☆24May 30, 2024Updated last year