User Manual
===========

Welcome to the user manual of `MetaGraph <https://metagraph.ethz.ch>`_!

This manual includes setup instructions and usage tutorials outlining the key use cases for the MetaGraph
framework, a software platform for indexing and analysis of very large sequence collections.

.. attention:: This documentation is currently under development (`source <https://github.com/ratschlab/metagraph/tree/master/metagraph/docs/source>`_). In case of specific questions or requests to extend certain sections of this manual, please do not hesitate to open an issue on `GitHub <https://github.com/ratschlab/metagraph>`_ or propose your changes via a pull request.

.. toctree::
   :maxdepth: 3

   installation.rst
   quick_start.rst
   workflows.rst
   api.rst
   sequence_search.rst
   sequence_assembly.rst
   resources.rst