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...

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...