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Parallelization, Scalability, and Reproducibility in Next-Generation Sequencing Analysis

Johannes Koster

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Tags: Algorithms, Bayesian, Bioinformatics, Biology, Filtering, Next-Generation sequencing, nVidia, nVidia GeForce GTX 580, nVidia GeForce GTX 780, OpenCL, Package, Thesis

March 23, 2015 by hgpu

SW#db: GPU-accelerated exact sequence similarity database search

Matija Korpar, Martin Sosic, Dino Blazeka, Mile Sikic

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Tags: Algorithms, Biology, CUDA, Databases, Next-Generation sequencing, nVidia, nVidia GeForce GTX 690, nVidia GeForce GTX 780, Package, Smith-Waterman algorithm

January 16, 2015 by hgpu

GPU-accelerated Computation for Statistical Analysis of the Next-Generation Sequencing Data

Yilan Liu

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Tags: Bioinformatics, Biology, Computer science, CUDA, Next-Generation sequencing, nVidia, nVidia GeForce GTX 770

June 13, 2014 by hgpu

cuBLASTP: Fine-Grained Parallelization of Protein Sequence Search on a GPU

Jing Zhang, Hao Wang, Heshan Lin, Wu-chun Feng

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Tags: Bioinformatics, Biology, CUDA, Next-Generation sequencing, nVidia, Sequence alignment, Tesla K20

May 23, 2014 by hgpu

SOAP3-dp: Fast, Accurate and Sensitive GPU-based Short Read Aligner

Ruibang Luo, Thomas Wong, Jianqiao Zhu, Chi-Man Liu, Edward Wu, Lap-Kei Lee, Haoxiang Lin, Wenjuan Zhu, David W. Cheung, Hing-Fung Ting, Siu-Ming Yiu, Chang Yu, Yingrui Li, Ruiqiang Li, Tak-Wah Lam

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Tags: Algorithms, Bioinformatics, Biology, CUDA, Next-Generation sequencing, nVidia, Package, Tesla C2070, Tesla M2050

February 25, 2013 by hgpu

G-SNPM – A GPU-based SNP mapping tool

Alessandro Orro, Andrea Manconi, Emanuele Manca, Giuliano Armano, Luciano Milanesi

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Tags: Algorithms, Bioinformatics, Biology, CUDA, Next-Generation sequencing, nVidia, nVidia GeForce GTX 480, Package, Python, Smith-Waterman algorithm

November 14, 2012 by hgpu

GHOSTM: A GPU-Accelerated Homology Search Tool for Metagenomics

Shuji Suzuki, Takashi Ishida, Ken Kurokawa, Yutaka Akiyama

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Tags: Algorithms, Biology, CUDA, Databases, Next-Generation sequencing, nVidia, Package, Tesla S1070

May 10, 2012 by hgpu

Exact and complete short-read alignment to microbial genomes using Graphics Processing Unit programming

Jochen Blom, Tobias Jakobi, Daniel Doppmeier, Sebastian Jaenicke, Jorn Kalinowski, Jens Stoye, Alexander Goesmann

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Tags: Algorithms, Bioinformatics, Biology, CUDA, Next-Generation sequencing, nVidia, Package

May 10, 2011 by hgpu

Exact and complete short read alignment to microbial genomes using GPU programming

Jochen Blom, Tobias Jakobi, Daniel Doppmeier, Sebastian Jaenicke, Jorn Kalinowski, Jens Stoye, Alexander Goesmann

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Tags: Bioinformatics, Biology, CUDA, Next-Generation sequencing, nVidia, nVidia GeForce GTX 280, Package

April 11, 2011 by hgpu

DecGPU: distributed error correction on massively parallel graphics processing units using CUDA and MPI

Yongchao Liu, Bertil Schmidt, Douglas Maskell

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Tags: Bioinformatics, Biology, CUDA, MPI, Next-Generation sequencing, nVidia, OpenMP, Package, Tesla S1070

April 11, 2011 by hgpu

GPU-RMAP: Accelerating Short-Read Mapping on Graphics Processors

Ashwin M. Aji, Liqing Zhang, Wu C. Feng

Tags: Bioinformatics, Biology, Next-Generation sequencing, nVidia

March 9, 2011 by hgpu

Monte Carlo randomization tests for large-scale abundance datasets on the GPU

John L. Van Hemert, Julie A. Dickerson

Tags: Bioinformatics, Biology, CUDA, Medicine, Metabolomics, Monte Carlo simulation, Next-Generation sequencing, nVidia

November 8, 2010 by hgpu

Boda: A C++ Framework for Efficient Experiments in Computer Vision [WIP]

Implementing Efficient, Portable Computations for Machine Learning

Parallel and in-process compilation of individuals for genetic programming on GPU

ESPRESO: Highly Parallel Solvers for Engineering Applications

Intel Xeon Phi acceleration of Hybrid Total FETI solver

MECCA development in accelerators - KPP Fortran to CUDA source-to-source pre-processor

MEDINA: MECCA Development in Accelerators – KPP Fortran to CUDA source-to-source Preprocessor

Internally-maintained tool for examining GPU scheduling behavior

Inferring the Scheduling Policies of an Embedded CUDA GPU

CLBlast: Tuned OpenCL BLAS

CLBlast: A Tuned OpenCL BLAS Library

Open source implementation of the PAAC algorithm presented in Efficient Parallel Methods for Deep Reinforcement Learning

Efficient Parallel Methods for Deep Reinforcement Learning

IDA*

Block-Parallel IDA* for GPUs

Repository for 1D Swept rule scheme written in CUDA C

Accelerating solutions of PDEs with GPU-based swept time-space decomposition

DeepMetabolism: a deep learning algorithm to predict phenotype from genome sequencing

DeepMetabolism: A Deep Learning System to Predict Phenotype from Genome Sequencing

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high performance computing on graphics processing units: hgpu.org

Parallelization, Scalability, and Reproducibility in Next-Generation Sequencing Analysis

SW#db: GPU-accelerated exact sequence similarity database search

GPU-accelerated Computation for Statistical Analysis of the Next-Generation Sequencing Data

cuBLASTP: Fine-Grained Parallelization of Protein Sequence Search on a GPU

SOAP3-dp: Fast, Accurate and Sensitive GPU-based Short Read Aligner

G-SNPM – A GPU-based SNP mapping tool

GHOSTM: A GPU-Accelerated Homology Search Tool for Metagenomics

Exact and complete short-read alignment to microbial genomes using Graphics Processing Unit programming

Exact and complete short read alignment to microbial genomes using GPU programming

DecGPU: distributed error correction on massively parallel graphics processing units using CUDA and MPI

GPU-RMAP: Accelerating Short-Read Mapping on Graphics Processors

Monte Carlo randomization tests for large-scale abundance datasets on the GPU

Recent source codes

Boda: A C++ Framework for Efficient Experiments in Computer Vision [WIP]

Parallel and in-process compilation of individuals for genetic programming on GPU

ESPRESO: Highly Parallel Solvers for Engineering Applications

MECCA development in accelerators - KPP Fortran to CUDA source-to-source pre-processor

Internally-maintained tool for examining GPU scheduling behavior

CLBlast: Tuned OpenCL BLAS

Open source implementation of the PAAC algorithm presented in Efficient Parallel Methods for Deep Reinforcement Learning

IDA*

Repository for 1D Swept rule scheme written in CUDA C

DeepMetabolism: a deep learning algorithm to predict phenotype from genome sequencing

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4th International Conference on Biomedical and Bioinformatics Engineering (ICBBE), 2017

9th International Conference on Signal Processing Systems (ICSPS), 2017

The 5th International conference on Control, Mechatronics and Automation (ICCMA), 2017

8th International Conference on Biology, Environment and Chemistry (ICBEC), 2017

2nd International Conference on Communication and Information Systems (ICCIS), 2017