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This feature is currently under active development. This will be release in the next OpenCGA 2.0
OpenCGA implements an Analysis Framework that allows the quick development of Native Analysis and Wrapped Analysis. Native analysis are written in Java and make Analysis make use of the internal OpenCGA APIs developedand threfore are implemented in Java, this allow a fast an easy implementation and the best scalability and performance. Some native analysis have implemented inside OpenCGA and are provided as part of OpenCGA. Users can develop also implement native analysis outside the OpenCGA source code as a plugin, this can easily installed in your OpenCGA installation.
Wrapped Analysis act as connectors to external binaries that can be implemented in any programming language, for instance PlinkWrappedAnalysis can query OpenCGA Variant Storage and export a PED/MAP or VCF file and execute Plink.
There are several native variant analysis implemented in OpenCGA, these use internal the different internal APIs developed to provide a scalable and high-performance implementation. Occasionally, these analysis can store results in the variant storage to allow users to filter by them, for instance GWAS analysis can be stored and/or indexed for filtering.
Variant Analysis aims aim to implement the most common genetic analysis, at the moment are implemented:
Clinical Interpretation Analysis
Clinical Interpretation Analysis allow to to discover variants or genes involved in
Custom Analysis (plugins)
User can easily install Native Analysis implemented externally to OpenCGA source code. We are considering creating a repository for the users. Tutorial , a tutorial is coming soon.
You can use external tools using the wrapper analysis. Some tools are being implemented naively and available to all users.
Users can easily extend and customise OpenCGA for their analysis.
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