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 8 months ago
- A fast, AVX2 and ARM Neon accelerated FM index library☆34Updated 10 months ago
- An efficient index for the colored, compacted, de Bruijn graph☆109Updated last year
- Histosketching Using Little Kmers☆56Updated 2 years ago
- Streaming algorithm for computing kmer statistics for massive genomics datasets☆54Updated 5 years ago
- Dashing 2 is a fast toolkit for k-mer and minimizer encoding, sketching, comparison, and indexing.☆66Updated last year
- Software accompanying "HINGE: Long-Read Assembly Achieves Optimal Repeat Resolution"☆63Updated 4 years ago
- Squeakr: An Exact and Approximate k -mer Counting System☆85Updated 7 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☆42Updated last year
- A repository for generating strobemers and evalaution☆78Updated last year
- Proof-of-concept implementation of GWFA for sequence-to-graph alignment☆55Updated last year
- HMM-guided metagenomic gene-targeted assembler using iterative de Bruijn graphs☆18Updated 9 years ago
- SAPLING: Suffix Array Piecewise Linear INdex for Genomics☆25Updated 5 years ago
- Ococo: the first online variant and consensus caller. Call genomic consensus directly from an unsorted SAM/BAM stream.☆46Updated 6 years ago
- ☆28Updated 6 months ago
- MinHash Alignment Process (MHAP, pronounced MAP): locality-sensitive hashing to detect long-read overlaps and utilities☆97Updated 3 years ago
- Arioc: GPU-accelerated DNA short-read alignment☆70Updated 4 months ago
- utilities for indexing and sequence extraction from FASTA files☆59Updated 4 years ago
- BELLA: a Computationally-Efficient and Highly-Accurate Long-Read to Long-Read Aligner and Overlapper☆50Updated 3 years ago
- Sensitive and Fast Alignment Search Tool for Long Read sequencing Data.☆41Updated 6 years ago
- De Bruijn graph representation in low memory☆35Updated last year
- tools for error correction and working with long read data☆44Updated 10 years ago
- Index kmtricks bf matrices☆45Updated this week
- a toolset for fast DNA read set matching and assembly using a new type of reduced kmer☆37Updated 4 years ago
- URMAP ultra-fast read mapper☆38Updated 5 years ago
- Symmetric DUST for finding low-complexity regions in DNA sequences☆45Updated 2 months ago
- A fast and space-efficient pre-filter for querying very large collections of nucleotide sequences.☆52Updated this week
- Antibiotic resistance predictions in minutes on a laptop☆50Updated 6 years ago
- Gfapy: a flexible and extensible software library for handling sequence graphs in Python☆69Updated 11 months ago