GobyWeb is a web application to aid with the analysis of high-throughput sequencing (HTS) data. In the back-end, it uses the Goby framework, BWA, STAR, Last, GSNAP, Samtools, VCF-tools, along with a cluster of servers to provide rapid alignment and efficient analyses. GobyWeb makes it possible to analyze hundreds of samples in consistent ways without having to use command line tools. GobyWeb provides tools that streamline frequent data analyses for RNA-Seq, Methyl-Seq, RRBS, or DNA-Seq datasets and to enable teams of investigators to share reads and results of analyses. GobyWeb can be extended for new analyses by developing plugins (see the GobyWeb Plugin SDK).

Citation and usage

If you have used GobyWeb in your work, please cite:

Kevin C. Dorff, Nyasha Chambwe, Zachary Zeno, Manuele Simi, Rita Shaknovich, and Fabien Campagne. GobyWeb: simplified management and analysis of gene expression and DNA methylation sequencing data. PLOS One, 2013, 10.1371/journal.pone.0069666.

See also the list of published studies that used GobyWeb.


CTSC GobyWeb Training

GobyWeb is available to investigators at our CTSC institutions who have an active subscription to the software (WMC, MSKCC, HSS, Hunter College, see GobyWeb subscription request form). We run training sessions monthly, registration instructions are sent by broadcast email. You can also sign up for training on these forms (level 1 training, level 2) or check out the GobyWeb training videos. Feel free to contact us if your project requires custom analyses or if you need to process large numbers of samples.

Project User Group

The GobyWeb user group is a good place to follow announcements of new features or ask questions about the software. You can also follow the lab software announcements on Twitter.

Download and installation

We have been offering non-commercial licenses of GobyWeb for download since version 1.6. Please see the software license, software requirements, and installation guide. These pages provide detailed installation instructions to setup local instances of GobyWeb. We would appreciate to hear from you if you are installing GobyWeb at your institution.

→ 2.3 (221 MB, Apr 18, 2014)

GobyWeb plugins are distributed under the LGPL3 open source license. See the GobyWeb Plugins SDK.


Alignment training video (see right menu for more video tutorials)

In addition to the video tutorials, here are detailed, but less interactive tutorials that describe how to perform some common RNA-Seq analyses using GobyWeb.

Introduction and File Formats

Uploading a Sample

Aligning samples to a reference genome

Packaging Alignments for Download

Differential Expression Analyses

Demonstration System

We have setup a demonstration system, uploaded public datasets and ran a number of gene expression and methylation analyses. Data and analysis results were shared with a guest account (login guest, password: guest), configured as a read-only user. You can access this demonstration system here.