high performance computing on graphics processing units: hgpu.org

hgpu.org » Sequence alignment

Migrating CUDA to oneAPI: A Smith-Waterman Case Study

Manuel Costanzo, Enzo Rucci, Carlos Garcia Sanchez, Marcelo Naiouf, Manuel Prieto-Matias

View

Tags: Bioinformatics, Biology, CUDA, FPGA, Heterogeneous systems, nVidia, nVidia GeForce GTX Titan X, nVidia GeForce RTX 2070, Sequence alignment, Smith-Waterman algorithm, SYCL

March 27, 2022 by hgpu

LOGAN: High-Performance GPU-Based X-Drop Long-Read Alignment

Alberto Zeni, Giulia Guidi, Marquita Ellis, Nan Ding, Marco D. Santambrogio, Steven Hofmeyr, Aydın Buluç, Leonid Oliker, Katherine Yelick

View

Download (PDF)

Source codes

Tags: Bioinformatics, Biology, CUDA, nVidia, Sequence alignment, Tesla V100

February 16, 2020 by hgpu

SneakySnake: A Fast and Accurate Universal Genome Pre-Alignment Filter for CPUs, GPUs, and FPGAs

Mohammed Alser, Taha Shahroodi, Juan Gomez-Luna, Can Alkan, Onur Mutlu

View

Download (PDF)

Source codes

Tags: Algorithms, Computer science, CUDA, FPGA, nVidia, Package, Sequence alignment

October 27, 2019 by hgpu

ASW: Accelerating Smith-Waterman Algorithm on Coupled CPU-GPU Architecture

Huihui Zou, Shanjiang Tang, Ce Yu, Hao Fu, Yusen Li, Wenjie Tang

View

Download (PDF)

Tags: Algorithms, APU, Bioinformatics, Biology, CUDA, Heterogeneous systems, nVidia, nVidia GeForce GTX 750, OpenCL, Sequence alignment, Smith-Waterman algorithm

December 9, 2018 by hgpu

pyPaSWAS: Python-based multi-core CPU and GPU sequence alignment

Sven Warris, N. Roshan N. Timal, Marcel Kempenaar, Arne M. Poortinga, Henri van de Geest, Ana L. Varbanescu, Jan-Peter Nap

View

Download (PDF)

Source codes

Tags: Bioinformatics, Biology, CUDA, nVidia, nVidia GeForce GTX 1070, OpenCL, Package, Python, Sequence alignment, Smith-Waterman algorithm

January 13, 2018 by hgpu

First Experiences Optimizing Smith-Waterman on Intel’s Knights Landing Processor

Enzo Rucci, Carlos Garcia, Guillermo Botella, Armando De Giusti, Marcelo Naiouf, Manuel Prieto-Matias

View

Download (PDF)

Tags: Bioinformatics, Biology, Computer science, Intel Xeon Phi, Sequence alignment, Smith-Waterman algorithm

February 26, 2017 by hgpu

Analysis and implementation of a BLAST-Like algorithm for MIC architectures

Felipe Sulser Larraz

View

Download (PDF)

Tags: Benchmarking, Bioinformatics, Biology, Computer science, Databases, Filtering, Intel Xeon Phi, Sequence alignment, Smith-Waterman algorithm, Thesis

February 2, 2017 by hgpu

Pairwise Sequence Alignment with Gaps with GPU

Thomas C. Carroll, Jude-Thaddeus Ojiaku, Prudence W.H. Wong

View

Download (PDF)

Tags: Algorithms, Bioinformatics, Biology, CUDA, nVidia, nVidia GeForce GTX 650, OpenCL, Sequence alignment

October 27, 2015 by hgpu

Accelerating Protein Structure Prediction using Particle Swarm Optimization on GPU

Hamed Khakzad, Yasaman Karami, Seyed Shahriar Arab

View

Download (PDF)

Tags: Algorithms, Bioinformatics, Biology, CUDA, nVidia, Particle swarm optimization, Sequence alignment, Tesla C1060

July 24, 2015 by hgpu

Improving the Mapping of Smith-Waterman Sequence Database Searches onto CUDA-Enabled GPUs

Liang-Tsung Huang, Chao-Chin Wu, Lien-Fu Lai, Yun-Ju Li

View

Download (PDF)

Tags: Bioinformatics, Biology, CUDA, Databases, nVidia, Sequence alignment, Smith-Waterman algorithm, Tesla C1060, Tesla K20

June 30, 2015 by hgpu

Concurrent Task Execution on the Intel Xeon Phi

Yucheng Zhu

View

Download (PDF)

Tags: Bioinformatics, Biology, Computer science, CUDA, Intel Xeon Phi, nVidia, OpenMP, Sequence alignment, Smith-Waterman algorithm, Tesla K20, Thesis

June 22, 2015 by hgpu

Comparative Study of the Parallelization of the Smith-Waterman Algorithm on OpenMP and Cuda C

Amadou Chaibou, Oumarou Sie

View

Download (PDF)

Tags: Bioinformatics, Biology, CUDA, nVidia, nVidia GeForce GTX 670, OpenMP, Sequence alignment, Smith-Waterman algorithm

June 22, 2015 by hgpu

* * *

GPJSON: GPU-based JSON data processing system accessible via all GraalVM languages

GPU-based JSON data processing using structural indexes

NEPTUNE: Network- and GPU-aware management of serverless functions at the edge

NEPTUNE: Network- and GPU-aware Management of Serverless Functions at the Edge

HeCBench: a collection of Heterogeneous Computing benchmarks written with CUDA, HIP, SYCL (DPC++), and OpenMP-4.5

Experience of Migrating a Parallel Graph Coloring Program from CUDA to SYCL

cuPSO: GPU Parallelization for Particle Swarm Optimization Algorithms

WARPSPEED: An analytic Data Volume and Performance Estimator for GPU Kernels

Analytical Performance Estimation during Code Generation on Modern GPUs

Celerity HLA: A high-level API on top of Celerity to support functional, C++20 range-adaptors-like patterns

The Celerity High-level API: C++20 for Accelerator Clusters

GPU-Sched

CASE: A Compiler-Assisted SchEduling Framework for Multi-GPU Systems

Efficient Execution of OpenMP on GPUs

Explicit Caching HYB based SpMV

Explicit caching HYB: a new high-performance SpMV framework on GPGPU

matrix_inversion algorithm

Performance study on GPU offloading techniques using the Gauss matrix inverse algorithm

See all packages

* * *

high performance computing on graphics processing units: hgpu.org

Migrating CUDA to oneAPI: A Smith-Waterman Case Study

LOGAN: High-Performance GPU-Based X-Drop Long-Read Alignment

SneakySnake: A Fast and Accurate Universal Genome Pre-Alignment Filter for CPUs, GPUs, and FPGAs

ASW: Accelerating Smith-Waterman Algorithm on Coupled CPU-GPU Architecture

pyPaSWAS: Python-based multi-core CPU and GPU sequence alignment

First Experiences Optimizing Smith-Waterman on Intel’s Knights Landing Processor

Analysis and implementation of a BLAST-Like algorithm for MIC architectures

Pairwise Sequence Alignment with Gaps with GPU

Accelerating Protein Structure Prediction using Particle Swarm Optimization on GPU

Improving the Mapping of Smith-Waterman Sequence Database Searches onto CUDA-Enabled GPUs

Concurrent Task Execution on the Intel Xeon Phi

Comparative Study of the Parallelization of the Smith-Waterman Algorithm on OpenMP and Cuda C

Recent source codes

GPJSON: GPU-based JSON data processing system accessible via all GraalVM languages

NEPTUNE: Network- and GPU-aware management of serverless functions at the edge

HeCBench: a collection of Heterogeneous Computing benchmarks written with CUDA, HIP, SYCL (DPC++), and OpenMP-4.5

cuPSO: GPU Parallelization for Particle Swarm Optimization Algorithms

WARPSPEED: An analytic Data Volume and Performance Estimator for GPU Kernels

Celerity HLA: A high-level API on top of Celerity to support functional, C++20 range-adaptors-like patterns

GPU-Sched

Efficient Execution of OpenMP on GPUs

Explicit Caching HYB based SpMV

matrix_inversion algorithm

Most viewed papers (last 30 days)