Web-Based Bioinformatics Workflows for RNA-Seq Data Analysis in Agricultural Animal Species

Remarkable advances in NGS technologies, bioinformatics algorithms and computational technologies have significantly accelerated genomic research. However, complicated NGS data analysis still remains as a major bottleneck in many projects. In order to address the computational challenges, we developed a bioinformatics web portal, which offers RNA-seq NGS data analysis for agriculturally important animal species.

We developed several integrated workflows that can perform end-to-end computational analysis, including sequence QC, reads mapping, transcriptome assembly and reconstruction and quantification, differential analysis, visualization and so on. One workflow mainly utilizes Tophat2, Cufflink, Cuffmerge and Cuffdiff suite of tools. Another workflow deploys Trinity for de novo assembly and uses RSEM for transcript quantification. Another workflow uses STAR and RSEM combination for computation. For all the workflows, he server supports analysis for multiple samples and multiple groups of samples and performs differential analysis between samples or groups, all in a single job submission. The calculated results are available for download and post analysis.

The supported animal species including chicken, cow, duck, goat guinea pig, horse rabbit, sheep, turkey, as wells as several other model organisms for validation purpose (fruit fly, human and yeast), whose genomic sequences and annotations are obtained from ENSEMBL.

The portal is implemented with many state-of-the-art HPC, workflow and web development software tools including Galaxy, StarCluster, OGS/GE utilizing modern scalable cloud compute and storage sources from AWS.

The RNA-seq portal is freely available from http://weizhongli-lab.org/RNA-seq.