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

摘要: We present GobyWeb, a web-based system that facilitates the management and analysis of high-throughput sequencing (HTS) projects. The software provides integrated support for broad set HTS analyses offers simple plugin extension mechanism. Analyses currently supported include quantification gene expression messenger small RNA sequencing, estimation DNA methylation (i.e., reduced bisulfite whole genome methyl-seq), or detection pathogens in sequenced data. In contrast to previous pipelines developed data, GobyWeb requires significantly less storage space, runs efficiently on parallel grid, scales gracefully process tens hundreds multi-gigabyte samples, yet can be used effectively by researchers who are comfortable using web browser. conducted performance evaluations found it either outperform have similar programs specialized most biologists took one-hour training session were readily able analyze RNA-Seq data with state art tools. obtained at http://gobyweb.campagnelab.org is freely available non-commercial use. plugins distributed source code licensed under open LGPL3 license facilitate inspection, reuse independent extensions http://github.com/CampagneLaboratory/gobyweb2-plugins.