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. RNA-seq, as one of the major area in the NGS field, also confronts great challenges in data analysis. In order to address the challenges in RNA-seq data analysis, we developed a bioinformatics web portal, which provides integrated RNA-seq pipelines for agriculturally important animal species.

This web portal offers three integrated workflows that can perform end-to-end computational analysis, including sequence quality control, reads mapping, transcriptome assembly, reconstruction and quantification, differential analysis, visualization and so on. The first workflow utilizes Tuxedo (Tophat, Cufflink, Cuffmerge and Cuffdiff suite of tools). The second workflow deploys Trinity for de novo assembly and uses RSEM for transcript quantification and EdgeR for differential analysis. The third combines STAR, RSEM, and EdgeR for data analysis. All these workflows support multiple samples and multiple groups of samples and perform differential analysis between groups in a single workflow job submission. The calculated results are available for download and post-analysis.

The supported animal species include chicken, cow, duck, goat, pig, horse, rabbit, sheep, turkey, as well as several other model organisms including yeast, C. elegans, fruitfly, zebrafish, mouse and human, with genomic sequences and annotations 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.