Fast and compact locality-preserving minimal perfect hashing for k-mer sets.
☆43Nov 18, 2023Updated 2 years ago
Alternatives and similar repositories for lphash
Users that are interested in lphash are comparing it to the libraries listed below
Sorting:
- Iterate k-min-mers from a DNA sequence in Rust☆13Apr 8, 2024Updated last year
- 📖 🧬 SSHash is a compressed, associative, exact, and weighted dictionary for k-mers.☆93Updated this week
- De Bruijn graph representation in low memory☆35Jul 6, 2024Updated last year
- ntHash implementation in Rust☆36Jul 12, 2024Updated last year
- Optimal distance lower bound k-mer sampling.☆12Jun 19, 2024Updated last year
- ☆21Dec 26, 2025Updated 2 months 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 3 months ago
- Bitpacked sequence trait and implementation☆16Jan 20, 2026Updated last month
- Next Index to Query Kmer Intersection☆17Feb 1, 2023Updated 3 years ago
- A minimal copy fastq and fasta reader built for parallel support and paired end processing☆42Jan 9, 2026Updated last month
- ☆24Apr 2, 2021Updated 4 years ago
- Generate kmers/minimizers/hashes/MinHash signatures, including with multiple kmer sizes.☆24Jan 9, 2021Updated 5 years ago
- semi-reference-based short read compression☆11Mar 5, 2019Updated 6 years ago
- SIMD-accelerated library for computing global and X-drop affine gap penalty sequence-to-sequence or sequence-to-profile alignments using …☆139Jun 23, 2024Updated last year
- Code for the paper Succinct k-mer Set Representations Using Subset Rank Queries on the Spectral Burrows-Wheeler Transform (SBWT)☆24Mar 13, 2025Updated 11 months ago
- Compacted and colored de Bruijn graph construction and querying☆92Updated this week
- Space-efficient pseudoalignment with a colored de Bruijn graph☆52Mar 13, 2025Updated 11 months ago
- Iterate over minimizers of a DNA sequence☆31Jul 12, 2024Updated last year
- Minimum plain text representation of kmer sets☆16Jan 30, 2025Updated last year
- A reimplementation of the WaveFront Alignment algorithm at low memory☆50May 22, 2024Updated last year
- ☆12Sep 7, 2019Updated 6 years ago
- a toolset for efficient analysis of 10X Genomics linked read data sets, in particular for de novo assembly☆15Nov 27, 2019Updated 6 years ago
- Code for the paper Aligning Distant Sequences to Graphs using Long Seed Sketches.☆13Nov 1, 2022Updated 3 years ago
- Implicit Interval Tree with Interpolation Index☆42Jul 13, 2022Updated 3 years ago
- A SIMD-accelerated library to compute random minimizers☆39Updated this week
- ProphAsm – a rapid computation of simplitigs directly from k-mer sets☆25Feb 17, 2023Updated 3 years ago
- Contains the description of a file format to store kmers and associated values☆34Aug 17, 2022Updated 3 years ago
- Fast, Cache-Efficient, and Scalable Queries on Pangenomes☆36Nov 7, 2025Updated 3 months ago
- Improved structural variant discovery in accurate long reads using sample-specific strings (SFS)☆49Sep 2, 2025Updated 6 months ago
- nimble aligner that will map your reads to the references on a laptop☆11Jun 29, 2017Updated 8 years ago
- Building the compacted de Bruijn graph efficiently from references or reads.☆92Feb 20, 2026Updated last week
- compacted de Bruijn graph construction in low memory☆100Nov 4, 2025Updated 3 months ago
- ⚡️ 🧬 Fulgor is a fast and space-efficient colored de Bruijn graph index.☆59Updated this week
- Histosketching Using Little Kmers☆56May 25, 2023Updated 2 years ago
- Cache-friendly, Parallel, and Samplesort-based Constructor for Suffix Arrays and LCP Arrays☆17Jun 23, 2025Updated 8 months ago
- ☆14Oct 14, 2020Updated 5 years ago
- Fast and Memory Efficient Genome Sketching via HyperLogLog, HyperMinHash and UltraLogLog☆19Jan 22, 2026Updated last month
- Fast approximate string searching☆100Updated this week
- Dashing 2 is a fast toolkit for k-mer and minimizer encoding, sketching, comparison, and indexing.☆70Jun 17, 2024Updated last year