GobyWeb: simplified management and analysis of gene expression and DNA methylation sequencing data
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.
Keywords
Cite
@article{arxiv.1211.6666,
title = {GobyWeb: simplified management and analysis of gene expression and DNA methylation sequencing data},
author = {Kevin C. Dorff and Nyasha Chambwe and Zachary Zeno and Rita Shaknovich and Fabien Campagne},
journal= {arXiv preprint arXiv:1211.6666},
year = {2015}
}
Comments
main manuscript: 17 pages, 4 tables, 6 figures. Supplementary material: 4 figures. Comment on this manuscript on Twitter or Google+ with this handle: #GobyWebPaper