GobyWeb: Simplified Management and Analysis of Gene Expression and DNA Methylation Sequencing Data

Kevin C. Dorff, Nyasha Chambwe, Zachary Zeno, Manuele Simi, Rita Shaknovich, Fabien Campagne, Nicholas James Provart
2013 PLoS ONE  
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
more » ... ta. 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.
doi:10.1371/journal.pone.0069666 pmid:23936070 pmcid:PMC3720652 fatcat:6otoosyouff5lehehqlvukdrji