CMU-SAFARI / Shifted-Hamming-DistanceLinks
Source code for the Shifted Hamming Distance (SHD) filtering mechanism for sequence alignment. Described in the Bioinformatics journal paper (2015) by Xin et al. at http://users.ece.cmu.edu/~omutlu/pub/shifted-hamming-distance_bioinformatics15_proofs.pdf
☆36Updated 5 years ago
Alternatives and similar repositories for Shifted-Hamming-Distance
Users that are interested in Shifted-Hamming-Distance are comparing it to the libraries listed below
Sorting:
- micro-read Fast Alignment Search Tool☆19Updated 6 years ago
- GateKeeper: Fast Alignment Filter for DNA Short Read Mapping☆21Updated 6 years ago
- COBS - Compact Bit-Sliced Signature Index (for Genomic k-Mer Data or q-Grams)☆87Updated last year
- Shouji is fast and accurate pre-alignment filter for banded sequence alignment calculation. Described in the Bioinformatics journal paper…☆18Updated 6 years ago
- ProbMinHash – A Class of Locality-Sensitive Hash Algorithms for the (Probability) Jaccard Similarity☆44Updated 5 years ago
- SneakySnake is the first and the only pre-alignment filtering algorithm that works efficiently and fast on modern CPU, FPGA, and GPU arch…☆53Updated 2 years ago
- LOGAN: High-Performance Multi-GPU X-Drop Long-Read Alignment.☆29Updated 3 years ago
- 📖 🧬 SSHash is a compressed, associative, exact, and weighted dictionary for k-mers.☆89Updated 2 weeks ago
- Bit packed vector of integral values☆28Updated 10 months ago
- ☆20Updated 5 years ago
- Fastq compression☆18Updated 6 years ago
- Hardware Acceleration of Long Read Pairwise Overlapping in Genome Sequencing: Open Source Repository☆33Updated last year
- Apollo is an assembly polishing algorithm that attempts to correct the errors in an assembly. It can take multiple set of reads in a sing…☆27Updated 5 years ago
- 🔶 Compressed bitvector/container supporting efficient random access and rank queries☆46Updated last year
- libsequence: a C++ class library for evolutionary genetic analysis☆53Updated 5 years ago
- FM-Index full-text index implementation using RRR Wavelet trees (libcds) and fast suffix sorting (libdivsufsort) including experimental r…☆107Updated 10 years ago
- NVBIO is a library of reusable components designed to accelerate bioinformatics applications using CUDA.☆58Updated 11 years ago
- Optimization of a Haplotype PairHMM class for GPU processing☆24Updated 8 years ago
- Simply feedforward neural network☆19Updated 9 years ago
- Source code for the software implementations of the GenASM algorithms proposed in our MICRO 2020 paper: Senol Cali et. al., "GenASM: A Hi…☆31Updated 2 years ago
- Ultra fast MSD radix sorter☆10Updated 5 years ago
- memory efficient, fast & precise taxnomomic classification system for metagenomic read mapping☆64Updated 6 months ago
- k8 Javascript shell☆158Updated last year
- An optimal space run-length Burrows-Wheeler transform full-text index☆65Updated 2 years ago
- Parallel String Graph Construction, Transitive Reduction, and Contig Generation for De Novo Genome Assembly☆16Updated last year
- C++ Implementations of sketch data structures with SIMD Parallelism, including Python bindings☆155Updated last year
- SetSketch: Filling the Gap between MinHash and HyperLogLog☆48Updated 4 years ago
- Building upon BWA-MEM2, this repository includes performance improvements to the seeding and mate-rescue steps.☆13Updated 4 years ago
- A C++14 library for NGS data formats☆39Updated 6 years ago
- An experimental tool to find approximate max-cuts in a large graph☆10Updated 4 years ago