> For the complete documentation index, see [llms.txt](https://docs.opencga.opencb.org/llms.txt). Markdown versions of documentation pages are available by appending `.md` to page URLs; this page is available as [Markdown](https://docs.opencga.opencb.org/develop-2/manual.md).

# User Manual

- [Installation](https://docs.opencga.opencb.org/develop-2/manual/installation.md)
- [Kubernetes Cluster](https://docs.opencga.opencb.org/develop-2/manual/installation/kubernetes.md)
- [Azure](https://docs.opencga.opencb.org/develop-2/manual/installation/kubernetes/azure.md)
- [Configuration](https://docs.opencga.opencb.org/develop-2/manual/installation/kubernetes/configuration.md)
- [On-Premise HPC Cluster](https://docs.opencga.opencb.org/develop-2/manual/installation/compute-cluster.md)
- [Server Configuration](https://docs.opencga.opencb.org/develop-2/manual/installation/compute-cluster/server-configuration.md)
- [Getting OpenCGA](https://docs.opencga.opencb.org/develop-2/manual/installation/compute-cluster/building-from-source.md)
- [Choosing Variant Storage Engine](https://docs.opencga.opencb.org/develop-2/manual/installation/compute-cluster/chosing-variant-storage.md): HBase vs. MongoDB
- [Configuration](https://docs.opencga.opencb.org/develop-2/manual/installation/compute-cluster/configuration.md)
- [Running Docker](https://docs.opencga.opencb.org/develop-2/manual/installation/docker.md)
- [Login](https://docs.opencga.opencb.org/develop-2/manual/login.md)
- [Using OpenCGA](https://docs.opencga.opencb.org/develop-2/manual/using-opencga.md): You can interact with your data in OpenCGA in several different ways, find the one that suits you most and get started!
- [REST Web Service API](https://docs.opencga.opencb.org/develop-2/manual/using-opencga/restful-web-service-api.md): Understanding REST web service API
- [IVA Web App](https://docs.opencga.opencb.org/develop-2/manual/using-opencga/iva-web-app.md): A rich web app front-end to work with OpenCGA
- [Client Libraries](https://docs.opencga.opencb.org/develop-2/manual/using-opencga/client-libraries.md): Java, Python, R and Javascript clients are implemented
- [pyopencga - Python Library](https://docs.opencga.opencb.org/develop-2/manual/using-opencga/client-libraries/python.md): If you're a Python user and you're keen of running OpenCGA through Python, you're in the right place!
- [opencgaR - R library](https://docs.opencga.opencb.org/develop-2/manual/using-opencga/client-libraries/r.md): If you're a R user and you're keen of running OpenCGA through R, you're in the right place!
- [Java](https://docs.opencga.opencb.org/develop-2/manual/using-opencga/client-libraries/java.md)
- [JavaScript](https://docs.opencga.opencb.org/develop-2/manual/using-opencga/client-libraries/javascript.md)
- [Command Line](https://docs.opencga.opencb.org/develop-2/manual/using-opencga/command-line.md)
- [Configuration](https://docs.opencga.opencb.org/develop-2/manual/using-opencga/command-line/configuration.md)
- [Files](https://docs.opencga.opencb.org/develop-2/manual/using-opencga/command-line/files.md): opencga.sh files
- [Public Demo](https://docs.opencga.opencb.org/develop-2/manual/using-opencga/public-demo.md)
- [Managing Data](https://docs.opencga.opencb.org/develop-2/manual/data-management.md)
- [Working with Projects and Studies](https://docs.opencga.opencb.org/develop-2/manual/data-management/projects-and-studies.md)
- [Loading of VCF files](https://docs.opencga.opencb.org/develop-2/manual/data-management/ingestion-of-vcf-files.md): This page describes the process that an operator follows to load their VCF files into an OpenCGA Variant Store.
- [Working with Files](https://docs.opencga.opencb.org/develop-2/manual/data-management/working-with-files.md)
- [Sharing and Permissions](https://docs.opencga.opencb.org/develop-2/manual/data-management/sharing-and-permissions.md)
- [Users and Groups](https://docs.opencga.opencb.org/develop-2/manual/data-management/sharing-and-permissions/users-and-groups.md)
- [Study ACLs](https://docs.opencga.opencb.org/develop-2/manual/data-management/sharing-and-permissions/permissions.md)
- [Population of metadata](https://docs.opencga.opencb.org/develop-2/manual/data-management/population-of-metadata.md)
- [Data Versioning](https://docs.opencga.opencb.org/develop-2/manual/data-management/population-of-metadata/data-versioning.md)
- [Adding Custom Metadata](https://docs.opencga.opencb.org/develop-2/manual/data-management/population-of-metadata/adding-custom-metadata.md)
- [Alignment Engine](https://docs.opencga.opencb.org/develop-2/manual/alignment-engine.md)
- [BAM Index](https://docs.opencga.opencb.org/develop-2/manual/alignment-engine/bam-index.md)
- [Alignment Read Query](https://docs.opencga.opencb.org/develop-2/manual/alignment-engine/alignment-read-query.md)
- [Working with Coverage](https://docs.opencga.opencb.org/develop-2/manual/alignment-engine/working-with-coverage.md)
- [Alignment Analysis](https://docs.opencga.opencb.org/develop-2/manual/alignment-engine/alignment-analysis.md)
- [Variant Storage Engine](https://docs.opencga.opencb.org/develop-2/manual/variant-storage-engine.md)
- [Variant Query](https://docs.opencga.opencb.org/develop-2/manual/variant-storage-engine/variant-query.md)
- [Variant Aggregation Stats](https://docs.opencga.opencb.org/develop-2/manual/variant-storage-engine/variant-aggregation-stats.md)
- [Variant Analysis](https://docs.opencga.opencb.org/develop-2/manual/variant-storage-engine/variant-analysis.md)
- [Clinical Genomics](https://docs.opencga.opencb.org/develop-2/manual/clinical-genomics.md)
- [Clinical Interpretation](https://docs.opencga.opencb.org/develop-2/manual/clinical-genomics/clinical-interpretation.md)
- [Clinical Analysis](https://docs.opencga.opencb.org/develop-2/manual/clinical-genomics/clinical-analysis.md)
- [Using JupyterLab](https://docs.opencga.opencb.org/develop-2/manual/using-jupyterlab.md)
- [Administrator](https://docs.opencga.opencb.org/develop-2/manual/administrator.md)
- [User Management](https://docs.opencga.opencb.org/develop-2/manual/administrator/user-management.md)
- [Templates / Manifest](https://docs.opencga.opencb.org/develop-2/manual/administrator/templates-manifest.md)