Accelerating edit-distance sequence alignment on GPU using the wavefront algorithm
Sequence alignment remains a fundamental problem with practical applications ranging
from pattern recognition to computational biology. Traditional algorithms based on dynamic …
from pattern recognition to computational biology. Traditional algorithms based on dynamic …
Implementation of the DWT in a GPU through a register-based strategy
P Enfedaque, F Auli-Llinas… - IEEE Transactions on …, 2014 - ieeexplore.ieee.org
The release of the CUDA Kepler architecture in March 2012 has provided Nvidia GPUs with
a larger register memory space and instructions for the communication of registers among …
a larger register memory space and instructions for the communication of registers among …
Boosting the FM-index on the GPU: Effective techniques to mitigate random memory access
The recent advent of high-throughput sequencing machines producing big amounts of short
reads has boosted the interest in efficient string searching techniques. As of today, many …
reads has boosted the interest in efficient string searching techniques. As of today, many …
Accelerating sequence alignments based on FM-index using the Intel KNL processor
JM Herruzo, S González-Navarro… - … ACM transactions on …, 2018 - ieeexplore.ieee.org
FM-index is a compact data structure suitable for fast matches of short reads to large
reference genomes. The matching algorithm using this index exhibits irregular memory …
reference genomes. The matching algorithm using this index exhibits irregular memory …
Compressed sparse FM-index: Fast sequence alignment using large k-steps
The FM-index is a data structure used in genomics for exact search of input sequences over
large reference genomes. Algorithms based on the FM-index show an irregular memory …
large reference genomes. Algorithms based on the FM-index show an irregular memory …
GPU-oriented architecture for an end-to-end image/video codec based on JPEG2000
C De Cea-Dominguez, JC Moure-Lopez… - IEEE …, 2020 - ieeexplore.ieee.org
Modern image and video compression standards employ computationally intensive
algorithms that provide advanced features to the coding system. Current standards often …
algorithms that provide advanced features to the coding system. Current standards often …
DART-PIM: DNA read mApping acceleRaTor Using Processing-In-Memory
R Ben-Hur, O Leitersdorf, R Ronen… - arXiv preprint arXiv …, 2024 - arxiv.org
Genome analysis has revolutionized fields such as personalized medicine and forensics.
Modern sequencing machines generate vast amounts of fragmented strings of genome data …
Modern sequencing machines generate vast amounts of fragmented strings of genome data …
Evaluation of genome alignment workflows on HPC processors
R Langarita Benítez - 2021 - upcommons.upc.edu
Precision medicine holds promise for improving healthcare by leveraging genomic
information. Due to the steep decrease in genome sequencing costs in recent years, the …
information. Due to the steep decrease in genome sequencing costs in recent years, the …
[PDF][PDF] Efficient approximate string matching techniques for sequence alignment
S Marco-Sola - 2017 - upcommons.upc.edu
One of the outstanding milestones achieved in recent years in the field of biotechnology
research has been the development of high-throughput sequencing (HTS). Due to the fact …
research has been the development of high-throughput sequencing (HTS). Due to the fact …
Accelerating pairwise sequence alignment on GPUs using the Wavefront Algorithm
Q Aguado Puig - 2022 - upcommons.upc.edu
Advances in genomics and sequencing technologies demand faster and more scalable
analysis methods that can process longer sequences with higher accuracy. However …
analysis methods that can process longer sequences with higher accuracy. However …