Open source platform for data analysis

Chipster is a user-friendly analysis software for high-throughput data developed by CSC, the Finnish IT Center for Science and ELIXIR node.

Chipster contains over 340 analysis tools for next generation sequencing (NGS), microarray, proteomics and sequence data. Users can save and share automatic analysis workflows, and visualize data interactively using a built-in genome browser and many other visualizations.

The data and the tools can be used either on command line, or via an intuitive graphic user interface, which also provides powerful visualizations, workflow functionality, and analysis metadata tracking.

Access policy

Chipster is open source, and the server environment is available as a virtual machine image free of charge. If you would like to use Chipster running on CSC’s server, you need a user account.

Chipster & EGI

Chipster relies on the EGI Federated Cloud for computing resources.

Additional technical details:

More information

Chipster is a service provided by CSC – IT Center for Science.

Use cases

Jussi Hepojoki, a virologist based at the University of Helsinki in Finland, used the Chipster platform to handle the millions of sequences generated by the NGS analysis of a deadly snake virus.

“I think that without CSC and Chipster, I would not have been able to carry out the sequence assembly. The power of ‘normal’ computers is just not enough for this type of work, or it takes a ridiculously lot of time.” J. Hepojoki


Kallio et al. 2011. Chipster: user-friendly analysis software for microarray and other high-throughput data BMC Genomics 12: 507 (open access)