Search Results for "cuda"
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Showing 18 open source projects for "cuda"
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CUDASW++: Smith-Waterman Algorithm
The fastest Smith-Waterman protein database search algorithm on GPUs
CUDASW++ software is a public open source software for Smith-Waterman protein database searches on Graphics Processing Units with CUDA. This software have been added to the NVIDIA Tesla Bio Workbench (http://www.nvidia.com/object/swplusplus_on_tesla.html -
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GPU MrBayes implements MrBayes MC(3) on the GPU using CUDA. When using our program in your article, please cite our paper "Efficient Implementation of MrBayes on multi-GPU" (http://mbe.oxfordjournals.org/content/early/2013/03/14/molbev.mst043.abstract.html?papetoc).
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This project, initially developed at University College London, contains programs to perform rigid, affine and non-linear registration of nifti or analyse images. Two versions of the algorithms are included, a CPU- and a GPU- (using CUDA) based implementation.
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Barracuda is a high-speed sequence aligner based on Sanger's BWA and utilizes the latest Nvidia CUDA architecture for accelerating alignments of sequence reads generated by next-generation sequencers.
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GPU3SNP
Exhaustive search for third order epistatic interactions using CUDA
GPU3SNP is a multi-GPU tool that exhaustively analyzes case-control datasets looking for 3-SNP combinations that present epistatic interaction. It provides a list with the combinations that have higher Mutual Information, which is used as measure for interaction. It is parallelized using CUDA and can exploit several GPUs in the same node/system. -
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LightSpMV
lightweight GPU-based sparse matrix-vector multiplication (SpMV)
LightSpMV is a novel CUDA-compatible sparse matrix-vector multiplication (SpMv) algorithm using the standard compressed sparse row (CSR) storage format. We have evaluated LightSpMV using various sparse matrices and further compared it to the CSR-based SpMV subprograms in the state-of-the-art CUSP and cuSPARSE. Performance evaluation reveals that on a single Tesla K40c GPU, LightSpMV is superior to both CUSP and cuSPARSE, with a speedup of up to 2.60 and 2.63 over CUSP, and up to 1.93 and 1.79 over cuSPARSE for single and double precision, respectively. -
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CUDAlign
CUDAlign is a tool that aligns huge DNA sequences in CUDA capable GPUs
CUDAlign is a tool able to align pairwise DNA sequences of unrestricted size in CUDA GPUs, using the Smith-Waterman algorithm combined with Myers-Miller. It produces the optimal alignment of 1 million base sequences in 45 seconds using a GTX 560 Ti. Many optimizations are being developed for this software. Look at the following papers for detailed information: [1] Edans Sandes, Alba Melo. Retrieving Smith-Waterman Alignments with Optimizations for Megabase Biological Sequences using GPU. ... -
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MSA-CUDA: multiple sequence aligner
multiple sequence alignment on CUDA-enabled GPUs.
This project is not active any more since we failed to get the permit from the Clustal team to distribute our software. You can refer to the paper "Yongchao Liu, Bertil Schmidt, Douglas L Maskell:MSA-CUDA: multiple sequence alignment on graphics processing units with CUDA. ASAP 2009" for more details. -
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birgHPCC
Rapid CUDA Cluster Deployment
...In short, birgHPCC is the world's first CUDA-ready, bioinformatics-based, live DVD. -
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Swift Sequence Alignment Program
GPU-based DNA sequence alignment program using Smith-Waterman
Swift is a DNA sequence alignment program that produces gapped alignment using the Smith-Waterman algorithm. It takes in a query file (FASTA format) and a reference file (FASTA format) as input. It outputs the reference name, read name, gapped alignment, alignment score, alignment start and end positions, and alignment length. I gave a talk on Swift in the GPU Technology Conference 2012. The talk can be accessed at... -
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DecGPU: CUDA-based Error Correction
The first distributed and parallel short-read error corrector on GPUs
DecGPU (Distributed Error correction on GPUs) is a parallel and distributed error correction algorithm for large-scale short read assembly. It is implemented using CUDA C++ and MPI, running on a GPU cluster. -
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CUSHAW: CUDA-based Short Read Alignment
the first aligner introducing a complete paired-end alignment on GPUs
CUSHAW is a CUDA compatible short read aligner to large genomes, such as the human genome, based on the Burrows Wheeler transform. -
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birgHPC is a Linux Live CD distribution based on PelicanHPC and Debian Live. birgHPC features automated cluster configuration on PCs in the same network specifically for bioinformatics and molecular dynamics. If you are looking for CUDA support, try birgHPCC (https://sourceforge.net/projects/birghpcc/) If you use birgHPC in your work, please cite us: Teong Han Chew, Kwee Hong Joyce-Tan, Farizuwana Akma and Mohd Shahir Shamsir. birgHPC: creating instant computing clusters for bioinformatics and molecular dynamics. Bioinformatics. Volume 27, Issue 9. pp 1320-1321. doi: 10.1093/bioinformatics/btr109
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This project shows how to integrate NVIDIA CUDA GPU programming API into ITK (Insight Segmentation and Registration Toolkit) library
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A fast parallel error correction tool for short reads. This software have been added to the NVIDIA Tesla Bio Workbench (http://www.nvidia.com/object/ec_on_tesla.html)
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Using the CUDA API this project modifies the AutoDock software to run in parallel on NVIDIA GPUs. Users will be able to download and compile the code and use AutoDock on CUDA capable Graphics Cards. Autodock is located at http://autodock.scripps.edu/
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Swallow
A Nondeterministic GLR Parser for CUDA
...This is where this project comes in. The many different possible interpretations, called parses, each of which produces a parse tree, are computed in parallel using the CUDA environment. Report on Stage 1 PDF http://tiny.cc/yp5qs HTML https://docs.google.com/document/pub?id=1iHpUBOPMwvJrWQHLHhUPHmU2t5KVieq25KItU-UbMpM&pli=1
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