svviz - a read visualizer for structural variants

svviz visualizes high-throughput sequencing data that supports a structural variant. svviz is free and open source, available at Please submit issues, questions or feature requests using the github issue tracker.

Visit the project page for a visual tour of the features, or continue through this documentation for more detailed information about svviz.



Oct, 2016 – svviz 1.6.0 as of version 1.6, svviz adds support for running under python 3.x in addition to python 2.7. I believe that the output should be identical (except for some very insignificant decimal places), but please report any anomalies or problems on the issue tracker.

Oct, 2016 – svviz 1.5.3 svviz 1.5.3 has been released. Upgrade using the following pip command: sudo pip install --upgrade svviz. You can see a list of the changes here.


  1. Install the latest version of svviz from github: sudo pip install svviz
  2. Run the following command: svviz demo

Detailed instructions, including how to ensure that all prerequisites are installed, are available on the Installation page.


svviz has been published in Bioinformatics. If you found svviz useful for your research, please cite svviz as follows:

Spies N, Zook JM, Salit M, Sidow A. 2015. svviz: a read viewer for validating structural variants. Bioinformatics doi:bioinformatics/btv478.

svviz was developed by Noah Spies, a member of the Sidow lab at Stanford and part of the Joint Initiative for Metrology in Biology (JIMB). Funding was provided by the National Institute of Standards and Technology (NIST).