jamshed / CaPS-SALinks
Cache-friendly, Parallel, and Samplesort-based Constructor for Suffix Arrays and LCP Arrays
☆15Updated 4 months ago
Alternatives and similar repositories for CaPS-SA
Users that are interested in CaPS-SA are comparing it to the libraries listed below
Sorting:
- Code for the paper Succinct k-mer Set Representations Using Subset Rank Queries on the Spectral Burrows-Wheeler Transform (SBWT)☆24Updated 7 months ago
- Fast, Cache-Efficient, and Scalable Queries on Pangenomes☆29Updated this week
- ☆16Updated 2 years ago
- Implementation of a Backpack Quotient Filter☆13Updated 3 months ago
- ⚡️ 🧬 Fulgor is a fast and space-efficient colored de Bruijn graph index.☆55Updated 2 weeks ago
- Reference implementations of minimizer schemes to go with the mod-minimizers paper.☆26Updated 6 months ago
- Fast and compact locality-preserving minimal perfect hashing for k-mer sets.☆43Updated last year
- Fast FASTA/Q parser and writer (C++ re-implementation of kseq library)☆53Updated last year
- Efficient construction of the BWT using string compression☆20Updated 4 months ago
- Space-efficient pseudoalignment with a colored de Bruijn graph☆52Updated 7 months ago
- Refinements of the WFA alignment algorithm with better complexity☆26Updated 3 years ago
- An experimental tool to find approximate max-cuts in a large graph☆10Updated 4 years ago
- SIMD-parallel BLAST X-drop DP on sequence graphs☆24Updated last year
- vector illustrations of BWT based searching on small strings☆16Updated 6 years ago
- GBWT in Rust☆42Updated 6 months ago
- ☆16Updated 2 years ago
- A hash map using the BooPHF perfect hash function☆13Updated 9 years ago
- Implementation of eBWT using Prefix-free parse (PFP)☆14Updated 3 months ago
- SAPLING: Suffix Array Piecewise Linear INdex for Genomics☆25Updated 5 years ago
- Optimal distance lower bound k-mer sampling.☆12Updated last year
- Optimal sequence-to-graph alignment with recombinations☆38Updated 3 months ago
- MONI: A Pangenomic Index for Finding MEMs☆37Updated 6 months ago
- KmerCamel🐫 provides implementations of several algorithms for efficiently representing a set of k-mers as a masked superstring.☆19Updated last month
- modular k-mer count matrix and Bloom filter construction for large read collections☆84Updated last month
- R-Index-F Library for Pattern Matching☆12Updated last year
- A reimplementation of the WaveFront Alignment algorithm at low memory☆49Updated last year
- FMSI is a highly memory efficient exact k-mer set index based on masked superstrings and the masked Burrows-Wheeler transform☆20Updated 3 months ago
- Compacted and colored de Bruijn graph construction and querying☆84Updated last week
- Rust implementation of VG handle graph☆19Updated last year
- ☆24Updated 4 years ago