OndrejSladky / kmercamelLinks
KmerCamel🐫 provides implementations of several algorithms for efficiently representing a set of k-mers as a masked superstring.
☆19Updated last month
Alternatives and similar repositories for kmercamel
Users that are interested in kmercamel are comparing it to the libraries listed below
Sorting:
- ⚡️ 🧬 Fulgor is a fast and space-efficient colored de Bruijn graph index.☆52Updated 2 weeks ago
- Reference implementations of minimizer schemes to go with the mod-minimizers paper.☆25Updated 3 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 weeks ago
- Alignment algorithm for short Illumina reads to a de Bruijn graph☆16Updated 6 years ago
- ☆13Updated 3 weeks ago
- A Rust library providing fully dynamic sets of k-mers with high locality☆45Updated 10 months ago
- Wavefront alignment algorithm (WFA) in Golang☆30Updated 2 weeks ago
- Fast and exact gap-affine partial order alignment☆53Updated 3 weeks ago
- base-accurate DNA sequence alignments using edlib and mashmap2☆33Updated 4 years ago
- ☆12Updated 8 months ago
- Long read aligner for cyclic and acyclic pangenome graphs☆39Updated last year
- A "Navie" Implementation of the Wavefront Algorithm For Sequence Alignment with Gap-Affine Scoring☆15Updated 2 years ago
- ProphAsm – a rapid computation of simplitigs directly from k-mer sets☆26Updated 2 years ago
- Iterate over minimizers of a DNA sequence☆31Updated last year
- Space-efficient pseudoalignment with a colored de Bruijn graph☆53Updated 4 months ago
- Iterate k-min-mers from a DNA sequence in Rust☆13Updated last year
- ☆17Updated 2 years ago
- MONI: A Pangenomic Index for Finding MEMs☆37Updated 4 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…☆11Updated 10 months ago
- GFAffix identifies walk-preserving shared affixes in variation graphs and collapses them into a non-redundant graph structure.☆37Updated 2 months ago
- RabbitMash: an efficient highly optimized implementation of Mash.☆21Updated last year
- COBS - Compact Bit-Sliced Signature Index (for Genomic k-Mer Data or q-Grams)☆20Updated 8 months ago
- Contains the description of a file format to store kmers and associated values☆32Updated 2 years ago
- A reimplementation of the WaveFront Alignment algorithm at low memory☆50Updated last year
- A k-mer search engine for all Sequence Read Archive public accessions☆31Updated 9 months ago
- syncmer graphs, and perhaps other sorts of sequence graphs☆21Updated 4 months ago
- Code for the paper Succinct k-mer Set Representations Using Subset Rank Queries on the Spectral Burrows-Wheeler Transform (SBWT)☆24Updated 4 months ago
- Dashing 2 is a fast toolkit for k-mer and minimizer encoding, sketching, comparison, and indexing.☆65Updated last year
- Compute a pairwise SNP distance matrix from one or two alignment(s)☆25Updated 10 months ago
- Next Index to Query Kmer Intersection☆16Updated 2 years ago