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
Alternatives and similar repositories for BLEND:
Users that are interested in BLEND are comparing it to the libraries listed below
- Scrooge is a high-performance pairwise sequence aligner based on the GenASM algorithm. Scrooge includes three novel algorithmic improveme…☆37Updated last year
- A versatile pairwise aligner for genomic and spliced nucleotide sequences☆18Updated last week
- GFA visualizer, GPU-accelerated using Vulkan☆69Updated 2 years ago
- Assemblies from HPP Year 1 production☆70Updated last year
- GPU implementation of the Wavefront Alignment Algorithm for global, gap-affine, pairwise sequence alginment☆30Updated 3 months ago
- AirLift is a tool that updates mapped reads from one reference genome to another. Unlike existing tools, It accounts for regions not shar…☆27Updated 7 months 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
- Efficient, parallel compression for terabyte-scale data☆36Updated this week
- RawHash can accurately and efficiently map raw nanopore signals to reference genomes of varying sizes (e.g., from viral to a human genome…☆51Updated last month
- BELLA: a Computationally-Efficient and Highly-Accurate Long-Read to Long-Read Aligner and Overlapper☆48Updated 2 years ago
- Parallel Sequence to Graph Alignment☆35Updated 2 years ago
- Proof-of-concept implementation of GWFA for sequence-to-graph alignment☆57Updated 7 months ago
- A Scalable GPU-Based Whole Genome Aligner, published in SC20: https://doi.ieeecomputersociety.org/10.1109/SC41405.2020.00043☆67Updated 5 months ago
- ☆12Updated 6 years ago
- Benchmarking pairwise aligners☆36Updated 9 months ago
- Alignment-free genotyper for SNPs and short indels, implemented in Python.☆48Updated 3 months ago
- Versatile simulator for structural variance and Nanopore/PacBio sequencing reads☆24Updated last year
- Refinements of the WFA alignment algorithm with better complexity☆26Updated 2 years ago
- C implementation of the Landau-Vishkin algorithm☆35Updated 2 years ago
- Snakemake pipeline for benchmarking read mappers☆16Updated last year
- A reimplementation of the WaveFront Alignment algorithm at low memory☆49Updated 7 months ago
- URMAP ultra-fast read mapper☆38Updated 4 years ago
- A C++ library and utilities for manipulating the Graphical Fragment Assembly format.☆52Updated 2 years ago
- MarginPolish: Graph based assembly polishing☆46Updated 4 years ago
- Optimized sequence graph implementations for graph genomics☆34Updated last month
- A versatile pairwise aligner for genomic and spliced nucleotide sequences☆51Updated 7 months ago
- MethPhaser: methylation-based haplotype phasing of human genomes☆43Updated 6 months ago
- A streaming method for mapping nanopore raw signals☆31Updated 3 years ago
- FastRemap, a C++ tool for quickly remapping reads between genome assemblies based on the commonly used CrossMap tool. Link to paper: http…☆26Updated 2 years ago