opencga | Open Computational Genomics Analysis platform for big data

 by   opencb Java Version: 2.12.0 License: Apache-2.0

kandi X-RAY | opencga Summary

kandi X-RAY | opencga Summary

opencga is a Java library typically used in Big Data, Spark applications. opencga has build file available, it has a Permissive License and it has low support. However opencga has 81 bugs and it has 6 vulnerabilities. You can download it from GitHub, Maven.

OpenCGA is an open-source project that aims to provide a Big Data storage engine and analysis framework for genomic scale data analysis of hundreds of terabytes or even petabytes. OpenCGA provides a scalable and high-performance Storage Engine framework to index biological data such as BAM or VCF files using different NoSQL databases, currently only MongoDB has been fully developed. A data analytics and genomic Analysis layer interface has been implemented over this big data storage index. A metadata Catalog has also been developed to provide authentification and ACLs and to keep track all of files and sample annotation. All these can be queried through a comprehensive RESTful web services API or using the command line interface. OpenCGA constitutes the big data analysis component of OpenCB initiative. It is used by other projects such as EMBL-EBI EVA, Babelomics or BierApp.

            kandi-support Support

              opencga has a low active ecosystem.
              It has 156 star(s) with 93 fork(s). There are 27 watchers for this library.
              There were 9 major release(s) in the last 6 months.
              There are 440 open issues and 1066 have been closed. On average issues are closed in 216 days. There are 10 open pull requests and 0 closed requests.
              It has a neutral sentiment in the developer community.
              The latest version of opencga is 2.12.0

            kandi-Quality Quality

              opencga has 81 bugs (23 blocker, 1 critical, 32 major, 25 minor) and 7453 code smells.

            kandi-Security Security

              opencga has no vulnerabilities reported, and its dependent libraries have no vulnerabilities reported.
              opencga code analysis shows 6 unresolved vulnerabilities (6 blocker, 0 critical, 0 major, 0 minor).
              There are 182 security hotspots that need review.

            kandi-License License

              opencga is licensed under the Apache-2.0 License. This license is Permissive.
              Permissive licenses have the least restrictions, and you can use them in most projects.

            kandi-Reuse Reuse

              opencga releases are available to install and integrate.
              Deployable package is available in Maven.
              Build file is available. You can build the component from source.
              Installation instructions, examples and code snippets are available.
              opencga saves you 135718 person hours of effort in developing the same functionality from scratch.
              It has 141837 lines of code, 9995 functions and 972 files.
              It has high code complexity. Code complexity directly impacts maintainability of the code.

            Top functions reviewed by kandi - BETA

            kandi has reviewed opencga and discovered the below as its top functions. This is intended to give you an instant insight into opencga implemented functionality, and help decide if they suit your requirements.
            • Converts a variant to a VariantSearchModel
            • Parse study query parameters .
            • Add query filters to a variant .
            • Pre processes the sample parameters .
            • Parse a sample index query from the given query .
            • handle a file link
            • Create a document containing a nested annotation .
            • Synchronize a collection of files .
            • Checks the annotation sets for the annotation set .
            • Merges the overlapping variants of the variant .
            Get all kandi verified functions for this library.

            opencga Key Features

            No Key Features are available at this moment for opencga.

            opencga Examples and Code Snippets

            No Code Snippets are available at this moment for opencga.

            Community Discussions

            Trending Discussions on opencga


            Function returns undefined in
            Asked 2021-Jan-07 at 23:17

            The following code works fine in a test.



            Answered 2021-Jan-07 at 14:45

            The problem is how to access variable in Cypress.

            This part of the doc should be helpfull


            I guess you can do something like this


            Community Discussions, Code Snippets contain sources that include Stack Exchange Network


            No vulnerabilities reported

            Install opencga

            OpenCGA is mainly developed in Java and it uses Apache Maven as building tool. OpenCGA requires Java 8, in particular JDK 1.8.0_60+, and other OpenCB dependencies that can be found in Maven Central Repository.
            java-common-libs: (branch 'develop')
            biodata: (branch 'develop')
            cellbase: (branch 'develop')
            oskar: (branch 'develop')
            You can build OpenCGA by executing the following command from the root of the cloned repository:.


            You can find OpenCGA documentation and tutorials at:
            Find more information at:

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          • HTTPS


          • CLI

            gh repo clone opencb/opencga

          • sshUrl


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