Documentation for gapseq
========================
gapseq is a program for the prediction and analysis of metabolic pathways and genome-scale networks.
This documentation covers software installation, basic use cases and sample workflows with focus on application.
For details on the biological and technical background please check the `gapseq publication <https://doi.org/10.1186/s13059-021-02295-1>`_.
In addition, the source is available at `github <https://github.com/jotech/gapseq>`_.

.. meta::
   :description lang=en: Informed prediction of bacterial metabolic pathways and reconstruction of accurate metabolic models 
   :keywords: metabolic networks, pathway analysis, constraint-based analysis, cobra, microbiology, metabolic interactions


Installation
------------
.. toctree::
   :maxdepth: 2

   /install


.. Usage
.. toctree::
   :maxdepth: 2
   :caption: Usage

   /usage/basics
   /usage/parameters
   /usage/medium
   /usage/output


.. Database
.. toctree::
   :maxdepth: 2
   :caption: Database

   /database/biochemistry
   /database/biomassReaction


.. Tutorials
.. toctree::
   :maxdepth: 1
   :caption: Tutorials

   /tutorials/crossfeeding
   /tutorials/yogurt
   /tutorials/archaea
   /tutorials/traceability


.. FAQ
.. toctree::
   :maxdepth: 2
   :caption: FAQ

   /faq
