GobyWeb is a web application to aid with the analysis of next-generation sequencing (NGS) data. In the back-end, it uses the Goby framework, BWA, GSNAP, last, 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 is available to investigators at our CTSC institutions (WMC, MSKCC, HSS, Hunter College). 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.

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

We have been offering non-commercial licenses of GobyWeb for download since version 1.6. The download page provides detailled installation instructions to setup local instances of GobyWeb. We would appreciate to hear from you if you are installing GobyWeb at your institution. Please contact us if you are interested in discussing licensing options or would like to evaluate the software for commercial use.

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