OndrejSladky / kmercamelLinks
KmerCamelπ« provides implementations of several algorithms for efficiently representing a set of k-mers as a masked superstring.
β19Updated 2 months ago
Alternatives and similar repositories for kmercamel
Users that are interested in kmercamel are comparing it to the libraries listed below
Sorting:
- β‘οΈ π§¬ Fulgor is a fast and space-efficient colored de Bruijn graph index.β55Updated last week
- Reference implementations of minimizer schemes to go with the mod-minimizers paper.β27Updated 6 months ago
- Iterate k-min-mers from a DNA sequence in Rustβ13Updated last year
- FMSI is a highly memory efficient exact k-mer set index based on masked superstrings and the masked Burrows-Wheeler transformβ20Updated 2 weeks ago
- COBS - Compact Bit-Sliced Signature Index (for Genomic k-Mer Data or q-Grams)β20Updated 11 months ago
- Iterate over minimizers of a DNA sequenceβ31Updated last year
- ProphAsm β a rapid computation of simplitigs directly from k-mer setsβ25Updated 2 years ago
- β13Updated last week
- Space-efficient pseudoalignment with a colored de Bruijn graphβ52Updated 8 months ago
- Contains the description of a file format to store kmers and associated valuesβ33Updated 3 years ago
- Optimal distance lower bound k-mer sampling.β12Updated last year
- A Rust library providing fully dynamic sets of k-mers with high localityβ46Updated last year
- Fast, Cache-Efficient, and Scalable Queries on Pangenomesβ34Updated last week
- RabbitMash: an efficient highly optimized implementation of Mash.β20Updated 2 years ago
- Code for the paper Succinct k-mer Set Representations Using Subset Rank Queries on the Spectral Burrows-Wheeler Transform (SBWT)β24Updated 8 months ago
- A "Navie" Implementation of the Wavefront Algorithm For Sequence Alignment with Gap-Affine Scoringβ14Updated 2 years ago
- Alignment algorithm for short Illumina reads to a de Bruijn graphβ17Updated 6 years ago
- Next Index to Query Kmer Intersectionβ16Updated 2 years ago
- Wavefront alignment algorithm (WFA) in Golangβ32Updated 3 months ago
- Benchmarking pairwise alignersβ36Updated 9 months ago
- β16Updated 2 years ago
- Sketch-based surveillance platformβ13Updated 10 months ago
- a toolset for fast DNA read set matching and assembly using a new type of reduced kmerβ37Updated 4 years ago
- A k-mer search engine for all Sequence Read Archive public accessionsβ35Updated last year
- Minimum plain text representation of kmer setsβ16Updated 9 months ago
- Optimal sequence-to-graph alignment with recombinationsβ38Updated 3 months ago
- Dividing heterogeneous long-read sequencing into groups with de Bruijn graphsβ31Updated last month
- Alignment against all pre-2019 bacteria on laptops within a few hours (former MOF-Search)β39Updated last year
- β16Updated 2 years ago
- fast, multithreaded sourmash operations: search, compare, and gather.β25Updated this week