fRNAkenseq: a Powered-by-iPlant RNA Sequencing Analysis Platform

We present fRNAkenseq: a novel, server based software platform for integrating multiple RNA sequencing analyses into a single Powered-by-iPlant platform with access to thousands of curated genome files.  Using iPlant’s computational resources and existing Powered by iPlant platforms, fRNAkenseq leverages the Tuxedo pipeline and several R Bioconductor packages into a scalable workflow that requires no prior computational experience.  fRNAkenseq is a complete fastq to enrichment analysis package, encompassing all stages of informatics processing.  Thus, it is an ideal tool for biologists and biostatisticians working with large-scale data.  Capitalizing on its integration with the Powered by iPlant Program and use of APIs, fRNAkenseq allows access to thousands of curated annotation and FASTA files of all species from the NCBI, BGI, Ensembl and JGI databases, making them easily available for RNAseq analysis. To our knowledge, this is the only RNAseq platform available which couples a diverse set of differential expression algorithms with a centralized infrastructure for data management.  Private genomes may also be uploaded through another iPlant platform, CoGe, and accessed for RNA-Seq analysis by fRNAkenseq. To aid the transition from data to insight, fRNAkenseq employs the visualization abilities of cummeRbund and provides access to pathway resources. By combining multiple analyses in a scalable fashion, fRNAkenseq provides a functional tool that enables researchers to select the most promising genes for further investigation from mRNA sequencing as well as manage the challengingly large sequence files.  In the future, fRNAkenseq will continue development for improved integration with iPlant computing infrastructure to allow cross talk with novel pathway resources and the iPlant datastore.