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Metadata and Security
Metadata Database
OpenCGA Catalog implements a high-performance metadata database to track all files metadata, samples, families, ...
Security
OpenCGA implements authentication to control what data can be seen by users. Data such as Files, Samples, Families, .. can be shared in different way.
Variant and Alignment Storage
Variant Database
OpenCGA implements a high-performance and scalable variant NoSQL database to store and index thousands of whole genome VCF files. Performance observed show more than 2,000 whole genomes indexed a day.
Many variant operations have been implemented such as variant aggregation, stats calculation, variant annotation, export, ...
We have implemented the most advanced query engine and aggregation framework to query variants.
Alignment Storage
Indexing BAM files and calculating coverage is supported. You can efficiently query all these data through REST web services.
Easy to Use
REST API and Clients
We have implemented a comprehensive REST API to work with Catalog and query Variants and Alignment data in a secure way. To facilitate using REST we have developed four client libraries developed in Java, Python, R and Javascript.
Command Line Interface
OpenCGA implements two different command lines, one for the users and one for the admin. Users can fully operate OpenCGA from the command line.
Clinical Analysis
Clinical Data and Disease Panels
You can store all you clinical data in our free data model solution in Catalog. You can define your clinical variables and annotate files, samples, individuals, families or cohort. Clinical Data is indexed automatically to provide a real-time queries and aggregations analysis.
Disease Panels are fully supported and versioned.
Clinical Interpretation Analysis
You can define different types of Clinical Analysis. We have implemented some automatic clinical interpretation algorithms for Rare Diseases (families) and Cancer. A Decision Support System has also been implemented in IVA.
Big Data Analysis
Rich Data Models
OpenCGA takes advantage of the rich data models developed in OpenCB. We make an extensive use of Variant and VariantAnnotation data models.
Spark Analysis
OpenCGA implements several analysis top of the Variant storage. These analysis can use different programming models – such as MapReduce – or different technologies such as Spark.
A Spark-based library has developed to provide extra analysis capabilities.
Visualisation
Source Code
Web based on IVA project at https://github.com/opencb/iva/tree/app/hgva
Server based on OpenCGA at https://github.com/opencb/opencga
Contributing
IVA is a collaborative project that aims to integrate as many reference human studies as possible, you can contact us for feature request. If you want to contribute to the code you are more than welcome to contribute to IVA and OpenCGA
Development
Contributors
Ignacio Medina (HPCS, University of Cambridge)
Source Code
Web based on IVA project at https://github.com/opencb/iva/tree/app/hgva
Server based on OpenCGA at https://github.com/opencb/opencga
Contributing
IVA is a collaborative project that aims to integrate as many reference human studies as possible, you can contact us for feature request. If you want to contribute to the code you are more than welcome to contribute to IVA and OpenCGA
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