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/…
☆51Updated 2 years ago
Alternatives and similar repositories for SneakySnake:
Users that are interested in SneakySnake are comparing it to the libraries listed below
- Hardware Acceleration of Long Read Pairwise Overlapping in Genome Sequencing: Open Source Repository☆33Updated 4 months ago
- Shouji is fast and accurate pre-alignment filter for banded sequence alignment calculation. Described in the Bioinformatics journal paper…☆17Updated 5 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…☆37Updated last year
- A benchmark suite to study the performance characteristics of genomics applications☆29Updated 5 months ago
- BLEND is a mechanism that can efficiently find fuzzy seed matches between sequences to significantly improve the performance and accuracy…☆43Updated last year
- 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
- Co-processor for whole genome alignment☆12Updated 4 years ago
- GateKeeper: Fast Alignment Filter for DNA Short Read Mapping☆18Updated 6 years ago
- 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
- RawHash can accurately and efficiently map raw nanopore signals to reference genomes of varying sizes (e.g., from viral to a human genome…☆55Updated 3 months ago
- GPU implementation of the Wavefront Alignment Algorithm for global, gap-affine, pairwise sequence alginment☆33Updated 6 months 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
- Falcon Accelerated Genomics Pipelines☆15Updated 5 years ago
- BELLA: a Computationally-Efficient and Highly-Accurate Long-Read to Long-Read Aligner and Overlapper☆49Updated 2 years ago
- generating hardware accelerators for pangenomic graph queries☆37Updated this week
- Building upon BWA-MEM2, this repository includes performance improvements to the seeding and mate-rescue steps.☆13Updated 3 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
- Optimization of a Haplotype PairHMM class for GPU processing☆24Updated 8 years ago
- GFA visualizer, GPU-accelerated using Vulkan☆70Updated 2 years ago
- ☆14Updated 4 months ago
- Proof-of-concept implementation of GWFA for sequence-to-graph alignment☆57Updated 10 months ago
- Global alignment and alignment extension☆131Updated last year
- A versatile pairwise aligner for genomic and spliced nucleotide sequences☆19Updated 2 months ago
- Optimized Dynamic Genome/Graph Implementation: understanding pangenome graphs☆204Updated last month
- Burrow-Wheeler Aligner for short-read alignment (see minimap2 for long-read alignment)☆17Updated last year
- slow5lib is a software library for reading & writing SLOW5 files.☆42Updated 2 months ago
- micro-read Fast Alignment Search Tool☆19Updated 5 years ago
- Refinements of the WFA alignment algorithm with better complexity☆26Updated 2 years ago
- CUDASW++4.0: Ultra-fast GPU-based Smith-Waterman Protein Sequence Database Search☆36Updated 4 months ago