high performance computing on graphics processing units: hgpu.org

hgpu.org » Sequence alignment

Accelerating bioinformatics applications on CUDA-enabled multi-GPU systems

Robin Kobus

View

Download (PDF)

Source codes

Tags: Bioinformatics, Biology, CUDA, Databases, Hashing, nVidia, nVidia Quadro GV100, Package, Sequence alignment, Tesla P100, Tesla V100, Thesis

November 27, 2023 by hgpu

minimap2-fpga: Integrating hardware-accelerated chaining for efficient end-to-end long-read sequence mapping

Kisaru Liyanage, Hiruna Samarakoon, Sri Parameswaran, Hasindu Gamaarachchi

View

Download (PDF)

Source codes

Tags: Bioinformatics, Biology, Cloud, FPGA, OpenCL, Package, Sequence alignment

June 11, 2023 by hgpu

SaLoBa: Maximizing Data Locality and Workload Balance for Fast Sequence Alignment on GPUs

Seongyeon Park, Hajin Kim, Tanveer Ahmad, Nauman Ahmed, Zaid Al-Ars, H. Peter Hofstee, Youngsok Kim, Jinho Lee

View

Download (PDF)

Tags: Bioinformatics, Biology, CUDA, Databases, nVidia, nVidia GeForce GTX 1650, nVidia GeForce RTX 3090, Sequence alignment, Smith-Waterman algorithm, String matching

January 29, 2023 by hgpu

Assessing Opportunities of SYCL and Intel oneAPI for Biological Sequence Alignment

Manuel Costanzo, Enzo Rucci, Carlos García Sánchez, Marcelo Naiouf, Manuel Prieto-Matías

View

Download (PDF)

Source codes

Tags: Bioinformatics, Biology, Computational biology, Computer science, CUDA, Heterogeneous systems, Intel, Intel UHD 630, nVidia, nVidia GeForce GTX 1080, nVidia GeForce GTX 980, nVidia GeForce RTX 2070, nVidia GeForce RTX 3090, OpenCL, Sequence alignment, SYCL, Tesla V100

November 27, 2022 by hgpu

Understanding the Power of Evolutionary Computation for GPU Code Optimization

Jhe-Yu Liou, Muaaz Awan, Steven Hofmeyr, Stephanie Forrest, Carole-Jean Wu

View

Download (PDF)

Source codes

Tags: Bioinformatics, Biology, Computer science, CUDA, Evolutionary Computations, Neural and Evolutionary Computing, nVidia, nVidia GeForce GTX 1080 Ti, Package, performance portability, Sequence alignment, Tesla P100, Tesla V100

September 4, 2022 by hgpu

AnySeq/GPU: A Novel Approach for Faster Sequence Alignment on GPUs

André Müller, Bertil Schmidt, Richard Membarth, Roland Leißa, Sebastian Hack

View

Download (PDF)

Source codes

Tags: AMD Radeon Instinct MI100, ATI, Bioinformatics, Biology, CUDA, Next-Generation sequencing, nVidia, nVidia GeForce RTX 3090, OpenCL, Package, Sequence alignment, Tesla A100

May 22, 2022 by hgpu

Migrating CUDA to oneAPI: A Smith-Waterman Case Study

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

View

Download (PDF)

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

Performance Study of GPU-based Joins

Efficiently Processing Large Relational Joins on GPUs

GenVectorX: A performance-portable SYCL library for Lorentz Vectors operations

bib boi: Tools to help with LaTeX paper writing

Compiler-centric across-stack deep learning acceleration

Kernel Tuner

Testing and Mutation Testing for GPU Kernels

CuPBoP-AMD: Extending CUDA to AMD Platforms

Creating a Dataset for High-Performance Computing Code Translation using LLMs: A Bridge Between OpenMP Fortran and C+

See all packages

* * *

high performance computing on graphics processing units: hgpu.org

Accelerating bioinformatics applications on CUDA-enabled multi-GPU systems

SaLoBa: Maximizing Data Locality and Workload Balance for Fast Sequence Alignment on GPUs

Assessing Opportunities of SYCL and Intel oneAPI for Biological Sequence Alignment

Understanding the Power of Evolutionary Computation for GPU Code Optimization

AnySeq/GPU: A Novel Approach for Faster Sequence Alignment on GPUs

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

Recent source codes

Performance Study of GPU-based Joins

GenVectorX: A performance-portable SYCL library for Lorentz Vectors operations

bib boi: Tools to help with LaTeX paper writing

Kernel Tuner

CuPBoP-AMD: Extending CUDA to AMD Platforms

gossip: Efficient Communication Primitives for Multi-GPU Systems

GT4Py: GridTools for Python

miniBUDE: A BUDE virtual-screening benchmark, in many programming models

AUCMEDI: a framework for Automated Classification of Medical Images

Creating a Dataset for High-Performance Computing Code Translation using LLMs: A Bridge Between OpenMP Fortran and C+

Most viewed papers (last 30 days)