GobyWeb: simplified management and analysis of gene expression and DNA methylation sequencing data

TL;DR

GobyWeb is a web-based platform that simplifies managing and analyzing large-scale high-throughput sequencing data, supporting various analyses with efficient storage and scalable processing.

Contribution

It introduces a user-friendly web system with integrated support for multiple HTS analyses and a plugin mechanism, reducing storage needs and enhancing scalability.

Findings

Supports gene expression and DNA methylation analysis

Runs efficiently on parallel grid systems

Scales to hundreds of large samples

Abstract

We present GobyWeb, a web-based system to facilitate the management and analysis of high-throughput sequencing (HTS) projects. The software provides integrated support for a broad set of HTS analyses and offers a simple plugin extension mechanism. Analyses currently supported include quantification of gene expression for messenger and small RNA sequencing, estimation of DNA methylation (i.e., reduced bisulfite sequencing and whole genome methyl-seq), or the detection of pathogens in sequenced data. In contrast to many analysis pipelines developed for analysis of HTS data, GobyWeb requires significantly less storage space, runs analyses efficiently on a parallel grid, scales gracefully to process tens or hundreds of multi-gigabyte samples, yet can be used effectively by researchers who are comfortable using a web browser. GobyWeb can be obtained at http://gobyweb.campagnelab.org and is freely available for non-commercial use.