===========================
Using a pathogen repository
===========================

This series of tutorials explains how to use an existing Nextstrain
:term:`pathogen repositories <pathogen repository>`. These tutorials explore
running workflows in Nextstrain pathogen repositories that are more complex than
the `example Zika workflow <https://github.com/nextstrain/zika-tutorial>`_
covered in the :doc:`earlier tutorial<../running-a-phylogenetic-workflow>`.

The tutorials will use the Nextstrain `Zika repository <https://github.com/nextstrain/zika>`_ as
an example pathogen repository and each one covers an individual :term:`workflow`
within the repository.

.. toctree::
   :maxdepth: 2
   :titlesonly:
   :caption: Table of contents

   running-an-ingest-workflow