torognes / swipeLinks
Smith-Waterman database searches with inter-sequence SIMD parallelisation
☆60Updated last year
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 7 months ago
- Squeakr: An Exact and Approximate k -mer Counting System☆85Updated 6 months ago
- An efficient index for the colored, compacted, de Bruijn graph☆110Updated 10 months ago
- Cosmo is a fast, low-memory DNA assembler using a Succinct (variable order) de Bruijn Graph.☆52Updated last year
- Fast and accurate set similarity estimation via containment min hash☆43Updated last year
- PacBio BAM C++ library☆21Updated 2 years ago
- HMM-guided metagenomic gene-targeted assembler using iterative de Bruijn graphs☆17Updated 8 years ago
- Dashing 2 is a fast toolkit for k-mer and minimizer encoding, sketching, comparison, and indexing.☆66Updated last year
- Histosketching Using Little Kmers☆57Updated 2 years ago
- A simple Partial Order Aligner based on Lee, Grasso and Sharlow (2002), for education/demonstration purposes☆74Updated last year
- Software accompanying "HINGE: Long-Read Assembly Achieves Optimal Repeat Resolution"☆64Updated 4 years ago
- tools for error correction and working with long read data☆44Updated 10 years ago
- Gfapy: a flexible and extensible software library for handling sequence graphs in Python☆68Updated 10 months ago
- A repository for generating strobemers and evalaution☆79Updated last year
- Ococo: the first online variant and consensus caller. Call genomic consensus directly from an unsorted SAM/BAM stream.☆47Updated 6 years ago
- Building the compacted de Bruijn graph efficiently from references or reads.☆89Updated 4 months ago
- Fast and accurate genomic distances using HyperLogLog☆163Updated 2 years ago
- Proof-of-concept implementation of GWFA for sequence-to-graph alignment☆57Updated last year
- Substring index for paths in a graph☆61Updated 4 months ago
- Arioc: GPU-accelerated DNA short-read alignment☆70Updated 3 months ago
- ☆37Updated 4 months ago
- Streaming algorithm for computing kmer statistics for massive genomics datasets☆54Updated 5 years ago
- A fast, AVX2 and ARM Neon accelerated FM index library☆34Updated 8 months ago
- Index kmtricks bf matrices☆45Updated 8 months ago
- Assembly Likelihood Estimator☆35Updated 2 years ago
- BELLA: a Computationally-Efficient and Highly-Accurate Long-Read to Long-Read Aligner and Overlapper☆50Updated 3 years ago
- BWT-based index for graphs☆72Updated 5 months ago
- online notebooks for a review of genome sketching☆61Updated 5 years ago
- Symmetric DUST for finding low-complexity regions in DNA sequences☆45Updated last month
- Sensitive and Fast Alignment Search Tool for Long Read sequencing Data.☆41Updated 6 years ago