RNAsik: A Pipeline for complete and reproducible RNA-seq analysis that runs anywhere with speed and ease

Abstract

RNA sequencing (RNA-seq) is one of many applications of high throughput sequencing, in which millions of short sequence reads, typically around 100 bases long, are produced from RNA samples with the aim of characterising entire transcriptomes. In order to analyse RNA-seq data, multiple bioinformatics tools are collected together into a pipeline, in which each tool accepts processed data from the previous tool as its input. The RNAsik pipeline streamlines processing of RNA-seq data and facilitates the production of reproducible results. This pipeline can run standalone on workstations, cloud instances, or on High Performance Computing (HPC) clusters. A single RNAsik run gives a comprehensive overview of the experiment and produces output suitable for Differential Gene Expression (DGE) analysis.