Reverse Engineering of TopHat: Splice Junction Mapper for Improving Computational Aspect

TopHat is a fast splice junction mapper for Next Generation Sequencing analysis, a technology for functional genomic research. Next Generation Sequencing technology allows more accurate analysis increasing data to elaborate, this opens to new challenges in terms of development of tools and computational infrastructures. We present a solution that cover aspects both software and hardware, the first one, after a reverse engineering phase, provides an improvement of algorithm of TopHat making it parallelizable, the second aspect is an implementation of an hybrid infrastructure: grid and virtual grid computing. Moreover the system allows to have a multi sample environment and is able to process automatically totally transparent to user.