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arXiv · 1211.6666

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

Kevin C. Dorff·Nyasha Chambwe·Zachary Zeno·Rita Shaknovich·Fabien Campagne
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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.

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Kevin C. Dorff, Nyasha Chambwe, Zachary Zeno, Rita Shaknovich, Fabien Campagne. 2012-11-28. GobyWeb: simplified management and analysis of gene expression and DNA methylation sequencing data. https://doi.org/10.1371/journal.pone.0069666

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