jamshed / CaPS-SA
Cache-friendly, Parallel, and Samplesort-based Constructor for Suffix Arrays and LCP Arrays
☆13Updated this week
Alternatives and similar repositories for CaPS-SA:
Users that are interested in CaPS-SA are comparing it to the libraries listed below
- Code for the paper Succinct k-mer Set Representations Using Subset Rank Queries on the Spectral Burrows-Wheeler Transform (SBWT)☆24Updated last week
- Implementation of a Backpack Quotient Filter☆11Updated 8 months ago
- Fast and cache-efficient full-text pangenome index☆27Updated 3 weeks ago
- Efficient construction of the BWT using string compression☆17Updated 5 months ago
- Reference implementations of minimizer schemes to go with the mod-minimizers paper.☆23Updated 3 weeks ago
- Fulgor is a fast and space-efficient colored de Bruijn graph index.☆49Updated 3 weeks ago
- Refinements of the WFA alignment algorithm with better complexity☆26Updated 2 years ago
- Space-efficient pseudoalignment with a colored de Bruijn graph☆53Updated last week
- SIMD-parallel BLAST X-drop DP on sequence graphs☆24Updated 9 months ago
- SAPLING: Suffix Array Piecewise Linear INdex for Genomics☆25Updated 4 years ago
- Fast and compact locality-preserving minimal perfect hashing for k-mer sets.☆43Updated last year
- A reimplementation of the WaveFront Alignment algorithm at low memory☆49Updated 10 months ago
- ☆8Updated 3 years ago
- ☆17Updated last year
- vector illustrations of BWT based searching on small strings☆16Updated 5 years ago
- An experimental tool to find approximate max-cuts in a large graph☆11Updated 3 years ago
- Optimal distance lower bound k-mer sampling.☆12Updated 9 months ago
- FMSI is a highly memory efficient exact k-mer set based on masked superstrings and the masked Burrows-Wheeler transform☆19Updated 2 months ago
- Contains the description of a file format to store kmers and associated values☆32Updated 2 years ago
- A Rust library providing fully dynamic sets of k-mers with high locality☆44Updated 5 months ago
- A tool for merging large BWTs☆26Updated 4 years ago
- Iterate k-min-mers from a DNA sequence in Rust☆13Updated 11 months ago
- MONI: A Pangenomic Index for Finding MEMs☆37Updated 5 months ago
- Fast and exact gap-affine partial order alignment☆49Updated 3 months ago
- KmerCamel🐫 provides implementations of several algorithms for efficiently representing a set of k-mers as a masked superstring.☆16Updated this week
- Optimal sequence-to-graph alignment with recombinations☆30Updated 3 weeks ago
- Self-contained, multi-threaded fasta/q parser☆43Updated 5 months ago
- a toolset for fast DNA read set matching and assembly using a new type of reduced kmer☆37Updated 3 years ago
- ☆25Updated 3 years ago
- Wavelet tree based on a fixed block boosting technique☆16Updated 3 years ago