JCVI launches a web portal for RNA-seq based gene expression analysis for agricultural animals

There is now a web portal that will provide the required tools and computing power for the research community to help drill down into the genetic make-up of horses. The portal was developed by scientists at the J. Craig Venter Institute, a non-profit genomics research institute in Maryland, in the United States.

The RNA-sequencing portal supports data processing for a range of agricultural animal species, including the horse, chicken, cow, duck, goat, pig, rabbit, sheep and turkey, as well as several other model organisms including yeast, C. elegans, Drosophila, and humans, with genomic sequences and annotations obtained from ENSEMBL.

The scientists have provided details of the new portal in the journal, BMC Genomics.

Weizhong Li, Alexander Richter, Yunsup Jung, Qiyun Zhu and Robert  Li said remarkable advances in Next Generation Sequencing (NGS)  technologies, bioinformatics algorithms and computational technologies had significantly accelerated genomic research.

However, complicated NGS data analysis still remained a major bottleneck, they noted. RNA-sequencing, as one of the major area in the NGS field, also faced great challenges in data analysis.

RNA sequencing, often referred to as RNA-seq and also called whole transcriptome shotgun sequencing, uses NGS to reveal the presence and quantity of RNA in a biological sample.

To address the challenges in RNA-sequencing data analysis, the authors developed a web portal that offers three integrated workflows that can perform end-to-end computing and analysis, including sequence quality control, read-mapping, transcriptome assembly, reconstruction and quantification, and differential analysis.

The first workflow utilizes Tuxedo (the 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.

Flowchart of the three workflows:


a Tuxedo workflow, b Trinity de-novo assembly and post-analysis workflow, and c STAR mapping and post analysis workflow

The portal is freely available for all users. The backend software package is also available as open-source software.

And the computing power? The whole computer system supporting the portal resides in the Amazon Web Services cloud environment. It runs on modern scalable cloud computing and storage sources.

While this is all very high-tech for the average horse owner, the upshot is rather simpler. RNA-sequencing is a very active field, the scientists noted, with many great analysis tools.

The aim of the project was not to develop new RNA-sequencing tools, but to build web workflows for using popular existing RNA-sequencing methods

“Our web portal makes available tools more accessible to the broader research community using RNA-seq technology but without access to either computer resources or expertise in bioinformatics.”

The scientists are with the J. Craig Venter Institute except for Robert Li, who is with the Animal Genomics and Improvement Laboratory, which is part of the US Department of Agriculture’s Agriculture Research Service.

Li W, R. Richter RA, Jung Y, Zhu Q, Li RW. (2016) Web-based bioinformatics workflows for end-to-end RNA-seq data computation and analysis in agricultural animal species. BMC Genomics 17:761. [article]

Source – Horsetalk.nz

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