CMU-SAFARI / SneakySnakeLinks
SneakySnake is the first and the only pre-alignment filtering algorithm that works efficiently and fast on modern CPU, FPGA, and GPU architectures. It greatly (by more than two orders of magnitude) expedites sequence alignment calculation for both short and long reads. Described in the Bioinformatics (2020) by Alser et al. https://arxiv.org/abs/…
☆52Updated 2 years ago
Alternatives and similar repositories for SneakySnake
Users that are interested in SneakySnake are comparing it to the libraries listed below
Sorting:
- Shouji is fast and accurate pre-alignment filter for banded sequence alignment calculation. Described in the Bioinformatics journal paper…☆17Updated 6 years ago
- Hardware Acceleration of Long Read Pairwise Overlapping in Genome Sequencing: Open Source Repository☆34Updated 7 months 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
- BLEND is a mechanism that can efficiently find fuzzy seed matches between sequences to significantly improve the performance and accuracy…☆43Updated 2 years ago
- A benchmark suite to study the performance characteristics of genomics applications☆32Updated 8 months 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
- BELLA: a Computationally-Efficient and Highly-Accurate Long-Read to Long-Read Aligner and Overlapper☆49Updated 3 years ago
- Source code of the processing-in-memory simulator used in the GRIM-Filter paper published at BMC Genomics in 2018: "GRIM-Filter: Fast See…☆11Updated 7 years ago
- Falcon Accelerated Genomics Pipelines☆15Updated 5 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 6 months ago
- Co-processor for whole genome alignment☆13Updated 5 years ago
- generating hardware accelerators for pangenomic graph queries☆38Updated this week
- GateKeeper: Fast Alignment Filter for DNA Short Read Mapping☆19Updated 6 years ago
- ☆14Updated 7 months ago
- GPU implementation of the Wavefront Alignment Algorithm for global, gap-affine, pairwise sequence alginment☆35Updated last month
- 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
- GFA visualizer, GPU-accelerated using Vulkan☆71Updated 2 years ago
- Source code for the software implementation of SeGraM proposed in our ISCA 2022 paper: Senol Cali et. al., "SeGraM: A Universal Hardware …☆12Updated 2 years ago
- micro-read Fast Alignment Search Tool☆19Updated 5 years ago
- Building upon BWA-MEM2, this repository includes performance improvements to the seeding and mate-rescue steps.☆13Updated 3 years ago
- A versatile pairwise aligner for genomic and spliced nucleotide sequences☆19Updated last month
- AIM, A Framework for High-throughput Sequence Alignment using Real Processing-in-Memory Systems, Bioinformatics, btad155, https://doi.or…☆22Updated 2 years ago
- Global alignment and alignment extension☆132Updated 2 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
- Optimization of a Haplotype PairHMM class for GPU processing☆24Updated 8 years ago
- Genome-on-Diet is a fast and memory-frugal framework for exemplifying sparsified genomics for read mapping, containment search, and metag…☆14Updated 9 months ago
- Optimized Dynamic Genome/Graph Implementation: understanding pangenome graphs☆213Updated last month
- Proof-of-concept implementation of GWFA for sequence-to-graph alignment☆57Updated last year
- A Scalable GPU-Based Whole Genome Aligner, published in SC20: https://doi.ieeecomputersociety.org/10.1109/SC41405.2020.00043☆72Updated 10 months ago