CMU-SAFARI / BLEND
BLEND is a mechanism that can efficiently find fuzzy seed matches between sequences to significantly improve the performance and accuracy while reducing the memory space usage of two important applications: 1) finding overlapping reads and 2) read mapping. Described by Firtina et al. (published in NARGAB https://doi.org/10.1093/nargab/lqad004)
☆42Updated last year
Related projects ⓘ
Alternatives and complementary repositories for BLEND
- Scrooge is a high-performance pairwise sequence aligner based on the GenASM algorithm. Scrooge includes three novel algorithmic improveme…☆37Updated last year
- ☆12Updated 5 years ago
- GPU implementation of the Wavefront Alignment Algorithm for global, gap-affine, pairwise sequence alginment☆28Updated last month
- GFA visualizer, GPU-accelerated using Vulkan☆68Updated 2 years ago
- Benchmarking pairwise aligners☆36Updated 7 months ago
- C implementation of the Landau-Vishkin algorithm☆35Updated 2 years ago
- 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 4 years ago
- A versatile pairwise aligner for genomic and spliced nucleotide sequences☆18Updated last month
- A reimplementation of the WaveFront Alignment algorithm at low memory☆49Updated 5 months ago
- Proof-of-concept implementation of GWFA for sequence-to-graph alignment☆56Updated 5 months ago
- Snakemake pipeline for benchmarking read mappers☆16Updated 11 months ago
- A streaming method for mapping nanopore raw signals☆31Updated 3 years ago
- MONI: A Pangenomic Index for Finding MEMs☆37Updated last month
- Parallel Sequence to Graph Alignment☆35Updated last year
- A Scalable GPU-Based Whole Genome Aligner, published in SC20: https://doi.ieeecomputersociety.org/10.1109/SC41405.2020.00043☆66Updated 3 months ago
- Pan-Genomic Matching Statistics☆48Updated 7 months ago
- A fuzzy Bruijn graph approach to long noisy reads assembly☆39Updated 7 years ago
- Refinements of the WFA alignment algorithm with better complexity☆26Updated 2 years ago
- Efficient low-divergence mapping of long reads in minimizer space☆63Updated last year
- MarginPolish: Graph based assembly polishing☆45Updated 3 years ago
- Fulgor is a fast and space-efficient colored de Bruijn graph index.☆44Updated this week
- A C++ library and utilities for manipulating the Graphical Fragment Assembly format.☆51Updated 2 years ago
- BELLA: a Computationally-Efficient and Highly-Accurate Long-Read to Long-Read Aligner and Overlapper☆48Updated 2 years ago
- REINDEER REad Index for abuNDancE quERy☆57Updated 3 months ago
- ☆26Updated 3 months ago
- Alignment-free genotyper for SNPs and short indels, implemented in Python.☆48Updated last month
- ☆27Updated 10 months ago
- SAPLING: Suffix Array Piecewise Linear INdex for Genomics☆25Updated 4 years ago
- ☆34Updated 4 years ago