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SW# – GPU enabled exact alignments on genome scale

Matija Korpar, Mile Sikic

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Tags: Bioinformatics, Biology, Computer science, CUDA, nVidia, nVidia GeForce GTX 560, nVidia GeForce GTX 570, nVidia GeForce GTX 690, Package, Sequence alignment, Smith-Waterman algorithm

April 23, 2013 by hgpu

CUDASW++ 3.0: accelerating Smith-Waterman protein database search by coupling CPU and GPU SIMD instructions

Yongchao Liu, Adrianto Wirawan, Bertil Schmidt

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Tags: Bioinformatics, Biology, CUDA, nVidia, nVidia GeForce GTX 680, nVidia GeForce GTX 690, Package, PTX, Sequence alignment, Smith-Waterman algorithm

April 10, 2013 by hgpu

Parallel Implementation of Dynamic Programming Algorithm Using Graphics Processing Unit

M. Khurram Rehman, M. Umer Sarwar, M. Ramzan Talib, M. Salman Mansoor, M. Bilal Sarwar

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Tags: Algorithms, Bioinformatics, Biology, Computer science, CUDA, Matrix multiplication, nVidia, nVidia GeForce GT 525 M, nVidia GeForce GT 610 M, Sequence alignment

April 6, 2013 by hgpu

GPU-Based Cloud Service for Smith-Waterman algorithm Using Frequency Distance Filtration Scheme

Sheng-Ta Lee, Chun-Yuan Lin, Che Lun Hung

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Tags: Bioinformatics, Biology, Cloud, CUDA, nVidia, Sequence alignment, Smith-Waterman algorithm, Tesla C2050

March 18, 2013 by hgpu

Binary Interval Search: a scalable algorithm for counting interval intersections

Ryan M. Layer, Kevin Skadron, Gabriel Robins, Ira M. Hall, Aaron R. Quinlan

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Tags: Algorithms, Bioinformatics, Biology, Computer science, CUDA, Monte Carlo simulation, nVidia, Package, Sequence alignment

February 6, 2013 by hgpu

Burrows-Wheeler Aligner: A Parallel Approach

Sheridan Lee Wright

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Tags: Algorithms, Bioinformatics, Biology, CUDA, MPI, nVidia, Sequence alignment, Thesis

January 16, 2013 by hgpu

High performance bioinformatics and computational biology on general-purpose graphics processing units

Cheng Ling

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Tags: Bioinformatics, Biology, Computational biology, CUDA, FPGA, nVidia, nVidia GeForce 8800 GTX, nVidia GeForce GTX 460, Sequence alignment, Thesis

January 3, 2013 by hgpu

GPU Acceleration of Pyrosequencing Noise Removal

Yang Gao, Jason D. Bakos

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Tags: Algorithms, Bioinformatics, Biology, Clustering, CUDA, MPI, nVidia, Sequence alignment, Tesla C2070

November 10, 2012 by hgpu

Accelerating the Smith-Waterman Algorithm for Bio-sequence Matching on GPU

Qianghua Zhu, Fei Xia, Guoqing Jin

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Tags: Algorithms, Bioinformatics, Biology, CUDA, Databases, nVidia, nVidia GeForce GTX 470, Sequence alignment, Sequence matching, Smith-Waterman algorithm

September 16, 2012 by hgpu

Binary Interval Search (BITS): A Scalable Algorithm for Counting Interval Intersections

Ryan M. Layer, Kevin Skadron, Gabriel Robins, Ira M. Hall, Aaron R. Quinlan

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Tags: Algorithms, Bioinformatics, Biology, Computer science, CUDA, nVidia, Package, Search, Sequence alignment

August 17, 2012 by hgpu

Algorithms for the mapping of genome sequences in GPGPU

David Seide

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Tags: Biology, CUDA, Genetics, nVidia, nVidia GeForce GTX 280, Sequence alignment, Thesis

August 5, 2012 by hgpu

An Algorithm for Fast Edit Distance Computation on GPUs

Reza Farivar, Harshit Kharbanda, Shivaram Venkataraman, Roy H. Campbell

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Tags: Algorithms, Bioinformatics, Biology, Computer science, CUDA, nVidia, nVidia GeForce GTX 275, Security, Sequence alignment

March 11, 2012 by hgpu

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Octo-Tiger: Astrophysics program simulating the evolution of star systems based on the fast multipole method on adaptive Octrees

Stellar Mergers with HPX-Kokkos and SYCL: Methods of using an Asynchronous Many-Task Runtime System with SYCL

BAT: A standardized benchmark suite for auto-tuners

Towards a Benchmarking Suite for Kernel Tuners

BenchDirect: A Directed Language Model for Compiler Benchmarks

A Deep Learning Model for Loop Interchange

Bridging Control-Centric and Data-Centric Optimization

Advanced evolutionary computation library built directly on top of PyTorch, created at NNAISENSE

EvoTorch: Scalable Evolutionary Computation in Python

See all packages

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high performance computing on graphics processing units: hgpu.org

SW# – GPU enabled exact alignments on genome scale

CUDASW++ 3.0: accelerating Smith-Waterman protein database search by coupling CPU and GPU SIMD instructions

Parallel Implementation of Dynamic Programming Algorithm Using Graphics Processing Unit

Binary Interval Search: a scalable algorithm for counting interval intersections

Burrows-Wheeler Aligner: A Parallel Approach

High performance bioinformatics and computational biology on general-purpose graphics processing units

GPU Acceleration of Pyrosequencing Noise Removal

Accelerating the Smith-Waterman Algorithm for Bio-sequence Matching on GPU

Binary Interval Search (BITS): A Scalable Algorithm for Counting Interval Intersections

Algorithms for the mapping of genome sequences in GPGPU

An Algorithm for Fast Edit Distance Computation on GPUs

Recent source codes

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Octo-Tiger: Astrophysics program simulating the evolution of star systems based on the fast multipole method on adaptive Octrees

BAT: A standardized benchmark suite for auto-tuners

BenchDirect: A Directed Language Model for Compiler Benchmarks

A Deep Learning Model for Loop Interchange

Bridging Control-Centric and Data-Centric Optimization

Advanced evolutionary computation library built directly on top of PyTorch, created at NNAISENSE

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