Goby is a next-gen data management framework designed to facilitate the implementation of efficient data analysis pipelines. The program is distributed under the GNU General Public License (GPL). The framework itself (goby-io) is distributed under the GNU Lesser General Public License (LGPL).


If you have used Goby in your work please cite:

Compression of structured high-throughput sequencing data. Campagne F, Dorff KC,  Chambwe N,  Robinson JT, Mesirov JP, PLoS ONE 2013 8(11): e79871. doi:10.1371/journal.pone.0079871 [PLoS ONE]

Goby provides very efficient file formats to store next-generation sequencing data and intermediary analysis results. The file formats are described in more detail in Campagne et al 2013.

Goby 1.x files were compressed with GZip.

In Goby 2.0, we introduced novel compression approaches that result in state of the art compression of alignment data. Goby 2.0 files can compress to a few percent of a BAM file and are often smaller than CRAM files. See what’s new in Goby 2.0.

Goby 3.0 introduces support for BAM and CRAM files, and provided deep-learning models for calling somatic variations.  See what’s new in Goby 3.0.

Goby also provides utilities that implement common next-gen data computations. We design these utilities to make them relatively easy to use, yet very efficient.

Interested in trying Goby? Here is how we recommend to proceed:

  1. Download the software.
  2. Need help, want to send suggestions? Address emails to goby-framework@googlegroups.com. You can also search this forum for answers to similar questions. Subscribing to the forum is also the best way to be notified of new releases.
  3. Configure on your computer.
  4. Take a look at the project tutorials, they discuss how to use Goby for different next-gen data analysis applications.
  5. Familiarize yourself with the various Goby modes (small utilities). Use java -jar goby.jar –help to display a list of modes. Help is context sensitive. Additional information can be found in the reference online manual.
  6. If you are a programmer interested in using Goby in your own projects, check out the project on GitHub.

Here are some tutorials that describe how to perform common NGS analysis tasks:

discover genomic variants Find  somatic mutations in samples, estimate allelelic frequencies, methylation rate, or and identify genomic positions where allele frequencies differ significantly between groups of samples.

import/Export SAM/BAM alignments Goby 2.0 provides very robust import/export capabilities for SAM/BAM format.

See the related pages listed on the right side of this page for an exhaustive list of pages about Goby. Looking for a web-based alignment and analysis tool? See GobyWeb, our grid-enabled web user interface.