UCLA-VAST / minimap2-accelerationLinks
Hardware Acceleration of Long Read Pairwise Overlapping in Genome Sequencing: Open Source Repository
☆34Updated 10 months ago
Alternatives and similar repositories for minimap2-acceleration
Users that are interested in minimap2-acceleration are comparing it to the libraries listed below
Sorting:
- SneakySnake is the first and the only pre-alignment filtering algorithm that works efficiently and fast on modern CPU, FPGA, and GPU arch…☆52Updated 2 years ago
- BLEND is a mechanism that can efficiently find fuzzy seed matches between sequences to significantly improve the performance and accuracy…☆43Updated 2 years ago
- LOGAN: High-Performance Multi-GPU X-Drop Long-Read Alignment.☆29Updated 2 years ago
- Scrooge is a high-performance pairwise sequence aligner based on the GenASM algorithm. Scrooge includes three novel algorithmic improveme…☆38Updated 2 years ago
- Shouji is fast and accurate pre-alignment filter for banded sequence alignment calculation. Described in the Bioinformatics journal paper…☆17Updated 6 years ago
- RawHash can accurately and efficiently map raw nanopore signals to reference genomes of varying sizes (e.g., from viral to a human genome…☆57Updated last month
- GPU implementation of the Wavefront Alignment Algorithm for global, gap-affine, pairwise sequence alginment☆36Updated 4 months ago
- BELLA: a Computationally-Efficient and Highly-Accurate Long-Read to Long-Read Aligner and Overlapper☆50Updated 3 years ago
- GFA visualizer, GPU-accelerated using Vulkan☆72Updated 3 years ago
- ☆49Updated 3 years ago
- A versatile pairwise aligner for genomic and spliced nucleotide sequences☆23Updated last week
- Falcon Accelerated Genomics Pipelines☆15Updated 5 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 5 years 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 last year
- generating hardware accelerators for pangenomic graph queries☆38Updated last month
- Optimized Dynamic Genome/Graph Implementation: understanding pangenome graphs☆218Updated last month
- A Scalable GPU-Based Whole Genome Aligner, published in SC20: https://doi.ieeecomputersociety.org/10.1109/SC41405.2020.00043☆70Updated last year
- Building upon BWA-MEM2, this repository includes performance improvements to the seeding and mate-rescue steps.☆13Updated 3 years ago
- mrsFAST: micro-read substitution-only Fast Alignment Search Tool☆28Updated 4 years ago
- Proof-of-concept implementation of GWFA for sequence-to-graph alignment☆55Updated last year
- Complements Minimap2 for a fast and efficient Read-Until pipeline☆12Updated 2 years ago
- Global alignment and alignment extension☆134Updated 2 years ago
- Assemblies from HPP Year 1 production☆76Updated 2 years ago
- Slow5tools is a toolkit for converting (FAST5 <-> SLOW5), compressing, viewing, indexing and manipulating data in SLOW5 format.☆99Updated last month
- ☆25Updated 4 years ago
- ☆12Updated 6 years ago
- PBSIM2: a simulator for long read sequencers with a novel generative model of quality scores☆73Updated 2 years ago
- Dynamic, adaptive sampling during nanopore sequencing☆35Updated 4 months ago
- GraphMap - A highly sensitive and accurate mapper for long, error-prone reads http://www.nature.com/ncomms/2016/160415/ncomms11307/full/n…☆68Updated 3 years ago
- Optimization of a Haplotype PairHMM class for GPU processing☆24Updated 8 years ago