A SURVEY ON NGS - SHORT READ ALIGNMENT IN HIGH PERFORMANCE COMPUTING

G. Raja, U. Srinivasulu Reddy

Abstract: Next generation sequencing (NGS) is a new area for generating massive genome sequencing data at high speed with low cost. Due to this, there are huge problems for data storage, analysis, and management. At NGS, Short Read Alignment is a fundamental problem and it has a lot of applications, such as genetic variation, whole genome sequencing, and personalized medicine. Recently, many tools and algorithms have been developed to align the short-reads in NGS. This paper, describes a short survey on NSG-short read alignment in particular High Performance Computing environment. The authors discussed the performance of the most widely used tools like (BOWITE, BWA, SOAP, CLOUDBURST, etc.). Based on the results, CLOUDBURST gives the best performance compare to other methods

Keywords: NGS, Short read alignment, Hash, Tries, Cloud computing, and GPGPU

DOI: https://doi.org/10.15623/ijret.2014.0327016