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

Sequence alignment forms an important backbone in many sequencing applications. A commonly used strategy for sequence alignment is an approximate string matching with a two-dimensional dynamic programming approach. Although some prior work has been conducted on GPU acceleration of a sequence alignment, we identify several shortcomings that limit...

GPU acceleration of Darwin read overlapper for de novo assembly of long DNA reads

BACKGROUND: In Overlap-Layout-Consensus (OLC) based de novo assembly, all reads must be compared with every other read to find overlaps. This makes the process rather slow and limits the practicality of using de novo assembly methods at a large scale in the field. Darwin is a fast and accurate read overlapper that can be used for de novo...

Accelerating DNA Variant Calling Algorithms on High Performance Computing Systems

Next generation sequencing (NGS) technologies have transformed the landscape of genomic research. With the significant advances in NGS technologies, DNA sequencing is more affordable and accessible than ever before. Meanwhile, many DNA sequence analysis tools have been developed to derive useful information from the raw sequencing data produced...

Efficient Acceleration of the Pair-HMMs Forward Algorithm for GATK HaplotypeCaller on Graphics Processing Units

GATK HaplotypeCaller (HC) is a popular variant caller, which is widely used to identify variants in complex genomes. However, due to its high variants detection accuracy, it suffers from long execution time. In GATK HC, the pair-HMMs forward algorithm accounts for a large percentage of the total execution time. This article proposes to...

An Efficient GPU-based de Bruijn Graph Construction Algorithm for Micro-Assembly

In order to improve the accuracy of indel detection, micro-assembly is used in multiple variant callers, such as the GATK HaplotypeCaller to reassemble reads in a specific region of the genome. Assembly is a computationally intensive process that causes runtime bottlenecks. In this paper, we propose a GPU-based de Bruijn graph construction...

GPU-accelerated CFD Simulations for Turbomachinery Design Optimization

Design optimization relies heavily on time-consuming simulations, especially when using gradient-free optimization methods. These methods require a large number of simulations in order to get a remarkable improvement over reference designs, which are nowadays based on the accumulated engineering knowledge already quite optimal.<br/>High...

Reduction of computing time for least-squares migration based on the Helmholtz equation by graphics processing units

In geophysical applications, the interest in least-squares migration (LSM) as an imaging algorithm is increasing due to the demand for more accurate solutions and the development of high-performance computing. The computational engine of LSM in this work is the numerical solution of the 3D Helmholtz equation in the frequency domain. The...

Reduction of computing time for least-squares migration based on the Helmholtz equation by graphics processing units

In geophysical applications, the interest in least-squares migration (LSM) as an imaging algorithm is increasing due to the demand for more accurate solutions and the development of high-performance computing. The computational engine of LSM in this work is the numerical solution of the 3D Helmholtz equation in the frequency domain. The...