OndrejSladky / kmercamelLinks
KmerCamel🐫 provides implementations of several algorithms for efficiently representing a set of k-mers as a masked superstring.
☆19Updated 3 weeks ago
Alternatives and similar repositories for kmercamel
Users that are interested in kmercamel are comparing it to the libraries listed below
Sorting:
- ProphAsm – a rapid computation of simplitigs directly from k-mer sets☆25Updated 2 years ago
- ⚡️ 🧬 Fulgor is a fast and space-efficient colored de Bruijn graph index.☆52Updated last week
- Reference implementations of minimizer schemes to go with the mod-minimizers paper.☆25Updated 5 months ago
- FMSI is a highly memory efficient exact k-mer set index based on masked superstrings and the masked Burrows-Wheeler transform☆20Updated 2 months ago
- Iterate k-min-mers from a DNA sequence in Rust☆13Updated last year
- Contains the description of a file format to store kmers and associated values☆33Updated 3 years ago
- ☆13Updated last month
- Code for the paper Succinct k-mer Set Representations Using Subset Rank Queries on the Spectral Burrows-Wheeler Transform (SBWT)☆24Updated 6 months ago
- Space-efficient pseudoalignment with a colored de Bruijn graph☆52Updated 6 months ago
- A Rust library providing fully dynamic sets of k-mers with high locality☆46Updated last year
- A "Navie" Implementation of the Wavefront Algorithm For Sequence Alignment with Gap-Affine Scoring☆14Updated 2 years ago
- Fast and cache-efficient full-text pangenome index☆29Updated this week
- Wavefront alignment algorithm (WFA) in Golang☆32Updated 2 months ago
- SIMD-parallel BLAST X-drop DP on sequence graphs☆24Updated last year
- RabbitMash: an efficient highly optimized implementation of Mash.☆20Updated last year
- Iterate over minimizers of a DNA sequence☆31Updated last year
- COBS - Compact Bit-Sliced Signature Index (for Genomic k-Mer Data or q-Grams)☆20Updated 10 months ago
- syncmer graphs, and perhaps other sorts of sequence graphs☆21Updated 6 months ago
- Compute a pairwise SNP distance matrix from one or two alignment(s)☆25Updated last year
- AlfaPang builds pangenome graphs without alignments or references.☆12Updated 3 months ago
- Minimum plain text representation of kmer sets☆16Updated 8 months ago
- convert variation graph alignments to coverage maps over nodes☆24Updated 3 months ago
- MONI: A Pangenomic Index for Finding MEMs☆37Updated 6 months ago
- Next Index to Query Kmer Intersection☆16Updated 2 years ago
- GFA insert into GenomicSQLite☆48Updated 4 years ago
- Sketch-based surveillance platform☆13Updated 9 months ago
- HyLight is a strain aware de novo assembly method based on the overlap-layout-consensus (OLC) paradigm that leverages the strengths of NG…☆12Updated last year
- Alignment algorithm for short Illumina reads to a de Bruijn graph☆17Updated 6 years ago
- a toolset for fast DNA read set matching and assembly using a new type of reduced kmer☆37Updated 4 years ago
- GBWT in Rust☆42Updated 6 months ago