torognes / swipeLinks
Smith-Waterman database searches with inter-sequence SIMD parallelisation
☆60Updated 2 years ago
Alternatives and similar repositories for swipe
Users that are interested in swipe are comparing it to the libraries listed below
Sorting:
- A fast constructor of the compressed de Bruijn graph from many genomes☆42Updated 2 weeks ago
- A simple Partial Order Aligner based on Lee, Grasso and Sharlow (2002), for education/demonstration purposes☆74Updated last year
- Squeakr: An Exact and Approximate k -mer Counting System☆85Updated 9 months ago
- Cosmo is a fast, low-memory DNA assembler using a Succinct (variable order) de Bruijn Graph.☆53Updated last year
- An efficient index for the colored, compacted, de Bruijn graph☆110Updated last year
- Streaming algorithm for computing kmer statistics for massive genomics datasets☆54Updated 5 years ago
- Software accompanying "HINGE: Long-Read Assembly Achieves Optimal Repeat Resolution"☆63Updated 5 years ago
- Dashing 2 is a fast toolkit for k-mer and minimizer encoding, sketching, comparison, and indexing.☆68Updated last year
- BWT-based index for graphs☆73Updated 9 months ago
- Fast and accurate set similarity estimation via containment min hash☆42Updated last year
- Histosketching Using Little Kmers☆56Updated 2 years ago
- MinHash Alignment Process (MHAP, pronounced MAP): locality-sensitive hashing to detect long-read overlaps and utilities☆98Updated 3 years ago
- ☆36Updated 7 months ago
- Enhanced Artificial Genome Engine: next generation sequencing reads simulator☆33Updated 5 years ago
- A C++ header-only library for reading Oxford Nanopore Fast5 files☆53Updated 3 years ago
- Proof-of-concept implementation of GWFA for sequence-to-graph alignment☆55Updated last year
- SIMD-parallel BLAST X-drop DP on sequence graphs☆24Updated last year
- HMM-guided metagenomic gene-targeted assembler using iterative de Bruijn graphs☆18Updated 9 years ago
- utilities for indexing and sequence extraction from FASTA files☆59Updated 4 years ago
- Ococo: the first online variant and consensus caller. Call genomic consensus directly from an unsorted SAM/BAM stream.☆46Updated 6 years ago
- Building the compacted de Bruijn graph efficiently from references or reads.☆90Updated 7 months ago
- SAPLING: Suffix Array Piecewise Linear INdex for Genomics☆25Updated 5 years ago
- compacted de Bruijn graph construction in low memory☆100Updated last month
- Index kmtricks bf matrices☆46Updated this week
- A fast, AVX2 and ARM Neon accelerated FM index library☆36Updated last year
- a toolset for fast DNA read set matching and assembly using a new type of reduced kmer☆37Updated 4 years ago
- A repository for generating strobemers and evalaution☆79Updated last year
- An Oxford Nanopore Basecaller☆70Updated 4 years ago
- Incremental construction of FM-index for DNA sequences☆72Updated last year
- online notebooks for a review of genome sketching☆60Updated 6 years ago