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.. codeauthor:: Shaloo Shalini <shaloo_shalini@yahoo.com>

Important

GenPipes User Survey

Please take a moment to answer these 3 questions about your GenPipes usage. This will help us prioritize new features and pipeline enhancements.

Click here to take the survey.

Thank you!

GenPipes |genpipes_version| Documentation

Note

GenPipes is sponsored by Canadian Centre for Computational Genomics (C3G).

C3G has created a distributed innovation node with broad expertise in bioinformatics. It offers bioinformatics analysis and HPC services for the life sciences research community. These services include customized and case-by-case analysis, along with an extensive suite of software solutions for the genomics community.

Welcome onboard GenPipes!

GenPipes is a flexible Python-based framework that facilitates the development and deployment of multi-step genomic workflows, optimized for High-Performance Computing (HPC) clusters and the cloud. It offers 14 open source, validated and scalable :ref:`pipelines<docs_pipeline_ref>` for various :ref:`genomics applications<docs_gp_usecases>`.

Tip

Fighting COVID-19

GenPipes offers CoVSeq pipeline and Nanopore_CoVSeq pipeline to help researchers sequence and detect mutations quickly to prevent the spread of new strains. See :ref:`GenPipes CoVSeq Pipeline User Guide<docs_gp_covseq>`, :ref:`GenPipes Nanopore CoVSeq Pipeline User Guide<docs_gp_nanopore_cov>` for details.

GenPipes documentation is organized to address the needs of new users as well as seasoned users and contributors. Refer to the :ref:`Documenatation Map<docs_genpipes_archmap>` for details on how GenPipes documentation is organized.

Table of Contents

.. toctree::
   :maxdepth: 1
   :caption: GenPipes
   :name: sec-general

   about/index
   get-started/gp_usecases
   faq/gp_faq


.. toctree::
   :maxdepth: 1
   :caption: Getting started
   :name: sec-learn

   get-started/index
   deploy/how_to_deploy_genpipes
   user_guide/user_guide
   tutorials/list_tutorials


.. toctree::
   :maxdepth: 1
   :caption: Support
   :name: sec-support

   support/how_to_get_support


.. toctree::
   :maxdepth: 1
   :caption: Community
   :name: sec-community

   community/contributing
   community/channels


.. toctree::
   :maxdepth: 1
   :caption: Resources
   :name: sec-resources

   resources/citation
   resources/publications
   resources/workshops
   resources/testdataset
   resources/compute_resources


.. toctree::
   :maxdepth: 1
   :caption: Development
   :name: sec-devel

   development/release_notes
   development/dev_guide
   development/troubleshooting_guide


.. toctree::
   :maxdepth: 1
   :caption: Documentation
   :name: sec-documentation

   documentation/about
   documentation/genpipes_doc_archmap
   documentation/docs_changelog