CMU-SAFARI / SneakySnake
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/…
☆50Updated last year
Alternatives and similar repositories for SneakySnake:
Users that are interested in SneakySnake are comparing it to the libraries listed below
- Shouji is fast and accurate pre-alignment filter for banded sequence alignment calculation. Described in the Bioinformatics journal paper…☆17Updated 5 years ago
- Hardware Acceleration of Long Read Pairwise Overlapping in Genome Sequencing: Open Source Repository☆33Updated 3 months ago
- LOGAN: High-Performance Multi-GPU X-Drop Long-Read Alignment.☆29Updated 2 years ago
- A benchmark suite to study the performance characteristics of genomics applications☆29Updated 4 months ago
- GateKeeper: Fast Alignment Filter for DNA Short Read Mapping☆18Updated 5 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
- BLEND is a mechanism that can efficiently find fuzzy seed matches between sequences to significantly improve the performance and accuracy…☆42Updated last year
- Scrooge is a high-performance pairwise sequence aligner based on the GenASM algorithm. Scrooge includes three novel algorithmic improveme…☆37Updated last year
- Source code for the software implementations of the GenASM algorithms proposed in our MICRO 2020 paper: Senol Cali et. al., "GenASM: A Hi…☆30Updated 2 years ago
- Co-processor for whole genome alignment☆12Updated 4 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…☆52Updated 2 months ago
- GPU implementation of the Wavefront Alignment Algorithm for global, gap-affine, pairwise sequence alginment☆31Updated 4 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
- Falcon Accelerated Genomics Pipelines☆15Updated 5 years ago
- Building upon BWA-MEM2, this repository includes performance improvements to the seeding and mate-rescue steps.☆13Updated 3 years ago
- generating hardware accelerators for pangenomic graph queries☆37Updated last month
- micro-read Fast Alignment Search Tool☆19Updated 5 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
- GFA visualizer, GPU-accelerated using Vulkan☆70Updated 2 years ago
- AIM, A Framework for High-throughput Sequence Alignment using Real Processing-in-Memory Systems, Bioinformatics, btad155, https://doi.or…☆21Updated last year
- Optimization of a Haplotype PairHMM class for GPU processing☆24Updated 8 years ago
- BELLA: a Computationally-Efficient and Highly-Accurate Long-Read to Long-Read Aligner and Overlapper☆48Updated 2 years ago
- A versatile pairwise aligner for genomic and spliced nucleotide sequences☆18Updated last month
- Proof-of-concept implementation of GWFA for sequence-to-graph alignment☆57Updated 8 months ago
- Refinements of the WFA alignment algorithm with better complexity☆26Updated 2 years ago
- Global alignment and alignment extension☆130Updated last year
- Genome-on-Diet is a fast and memory-frugal framework for exemplifying sparsified genomics for read mapping, containment search, and metag…☆14Updated 5 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 8 months ago
- Optimized Dynamic Genome/Graph Implementation: understanding pangenome graphs☆203Updated last week
- Parallel String Graph Construction, Transitive Reduction, and Contig Generation for De Novo Genome Assembly☆15Updated 8 months ago