HPC-REDItools: a novel HPC-aware tool for improved large scale RNA-editing analysis

摘要

Advances in next generation sequencing (NGS) technologies have led to the production of an unprecedented amount of omic data (including genomes, transcriptomes, epigenomes from cells, tissues and organisms) changing science and medicine in ways never seen before and entering the “big data” era. The scale and efficiency of NGS poses the relevant challenges of sharing, archiving, integrating and analyzing these vast collections of omic data. Although tools and algorithms to handle and analyse large NGS datasets are now appearing, widespread software for common NGS analyses are yet multi-threaded or serial and not ready for the “big data” era revolution. As a consequence, the investigation of specific and important biological phenomena in large NGS datasets from international projects - such as The Cancer Genome Atlas (TCGA) [ ] or The Genotype-Tissue Expression project (GTEx) [ ] - is somehow precluded and, thus, a thorough redesign of algorithms and efficient implementations on High Performance Computing (HPC) infrastructures are mandatory [ ]. Hereafter, we introduce and describe HPC-REDItools, a HPC tool for accurate detection of RNA-editing events from large data repositories.