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...

Exploration of Alternative GPU Implementations of the Pair-HMMs Forward Algorithm

In order to handle the massive raw data generated by next generation sequencing (NGS) platforms, GPUs are widely used by many genetic analysis tools to speed up the used algorithms. In this paper, we use GPUs to accelerate the pair-HMMs forward algorithm, which is used to calculate the overall alignment probability in many genomics analysis...

RTL Implementation of an Optical Flow Algorithm (Lucas) Using the Catapult C High-Level Synthesis tool

With the development of the technology, today's digital systems' growing design complexity has outpaced the traditional RTL design flow. The manual steps of micro-architecture definition, hand written RTL, simulation, debug and area/speed optimization through RTL synthesis are becoming more and more time consuming that gives the call of higher...

Bandwidth Analysis of Functional Interconnects Used as Test Access Mechanism

Test data travels through a System on Chip (SOC) from the chip pins to the Core-Under-Test (CUT) and vice versa via a Test Access Mechanism (TAM). Conventionally, a TAM is implemented using dedicated communication infrastructure. However, also existing functional interconnect, such as a bus or Network on Chip (NOC), can be reused as TAM; this...

The Strength of Preference

Growth and preferential attachment are the two ingredients of the scale-free network. Based on the Barabási-Albert scale-free model, we construct a more general model by replacing the linear preferential attachment with the nonlinear preferential attachment. We introduce different networks by controlling a parameter ? which decides the...