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A Getting Started Guide to the Genomic Epidemiology of SARS-CoV-2
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This is the documentation for the SARS-CoV-2 workflow maintained and actively used by the Nextstrain core team.

In addition to the phylogenetic analysis described here, you can use `Nextclade <https://clades.nextstrain.org>`_ our "drag-and-drop" tool for clade assignment, mutation calling, and sequence quality control at `clades.nextstrain.org <https://clades.nextstrain.org/>`_.

If something in this documentation is broken or unclear, `open an issue <https://github.com/nextstrain/ncov/issues/new/choose>`_ so we can improve it for everyone.

If you have a specific question, `post a note on the discussion board <https://discussion.nextstrain.org/>`_ -- we're happy to help!

.. toctree::
    :maxdepth: 1
    :titlesonly:
    :caption: Tutorials
    :hidden:

    tutorial/intro
    tutorial/setup
    tutorial/example-data
    tutorial/custom-data
    tutorial/genomic-surveillance
    tutorial/next-steps
    tutorial/videos


.. toctree::
   :maxdepth: 1
   :titlesonly:
   :caption: Visualization & Interpretation
   :hidden:

   visualization/sharing
   visualization/interpretation
   visualization/narratives

.. toctree::
   :maxdepth: 1
   :titlesonly:
   :caption: Guides
   :hidden:

   guides/update-workflow
   guides/data-prep/index
   guides/workflow-config-file
   guides/customizing-visualization
   guides/run-analysis-on-terra

.. toctree::
   :maxdepth: 1
   :caption: Reference
   :hidden:

   reference/nextstrain-overview
   reference/files
   reference/workflow-config-file
   reference/remote_inputs
   reference/metadata-fields
   reference/naming_clades
   reference/data_submitter_faq
   reference/troubleshoot
   reference/change_log
   reference/glossary

.. toctree::
   :maxdepth: 1
   :titlesonly:
   :hidden:

   Stuck? Ask us on the discussion board. We're happy to help! <https://discussion.nextstrain.org/>