biointec / columbaLinks
Fast Approximate Pattern Matching using Search Schemes
☆16Updated this week
Alternatives and similar repositories for columba
Users that are interested in columba 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
- SIMD-parallel BLAST X-drop DP on sequence graphs☆24Updated last year
- a toolset for fast DNA read set matching and assembly using a new type of reduced kmer☆37Updated 4 years ago
- ☆14Updated 5 years ago
- Refinements of the WFA alignment algorithm with better complexity☆26Updated 3 years ago
- ☆17Updated 2 years ago
- FMSI is a highly memory efficient exact k-mer set index based on masked superstrings and the masked Burrows-Wheeler transform☆20Updated this week
- Fast and compact locality-preserving minimal perfect hashing for k-mer sets.☆43Updated last year
- A Rust library providing fully dynamic sets of k-mers with high locality☆46Updated last year
- Optimal distance lower bound k-mer sampling.☆12Updated last year
- Contains the description of a file format to store kmers and associated values☆33Updated 3 years ago
- A SIMD-accelerated library to compute random minimizers☆33Updated last week
- ProphAsm – a rapid computation of simplitigs directly from k-mer sets☆25Updated 2 years ago
- Header-only, gzread-like reader for gzip, bz2, and xz.☆11Updated 7 years ago
- Command line tools for IntSpan related bioinformatics operations☆12Updated 6 months ago
- Pairwise nucleotide alignment benchmark of Rust bindings☆30Updated 2 years ago
- Host depletion optimised for clinical metagenomic sequencing applications☆16Updated 11 months ago
- ☆24Updated 4 years ago
- De Bruijn graph representation in low memory☆35Updated last year
- A rust wrapper for the spoa C++ partial order alignment library☆10Updated 4 months ago
- ☆28Updated 6 months ago
- Rust library for processing sequencing reads.☆25Updated last year
- Reference implementations of minimizer schemes to go with the mod-minimizers paper.☆26Updated 6 months ago
- Fast, Cache-Efficient, and Scalable Queries on Pangenomes☆29Updated this week
- An experimental tool to find approximate max-cuts in a large graph☆10Updated 4 years ago
- nimble aligner that will map your reads to the references on a laptop☆11Updated 8 years ago
- ☆24Updated 2 months ago
- A bit-packed k-mer representation (and relevant utilities) for rust☆47Updated last year
- A fast and space-efficient pre-filter for estimating the quantification of very large collections of nucleotide sequences☆14Updated last week
- Efficient C functions to compute the summary statistics (flagstats) for sequencing read sets.☆15Updated 5 years ago