Welcome to SchemaRefinery's documentation!
==========================================

.. toctree::
   :maxdepth: 1
   :caption: Overview:

   SchemaRefinery/Overview/Overview
   SchemaRefinery/Overview/Installation
   SchemaRefinery/Overview/Contacts

.. toctree::
   :maxdepth: 1
   :caption: Modules:

   SchemaRefinery/Modules/DownloadAssemblies
   SchemaRefinery/Modules/AdaptLoci
   SchemaRefinery/Modules/MatchSchemas
   SchemaRefinery/Modules/IdentifyParalogousLoci
   SchemaRefinery/Modules/IdentifySpuriousGenes
   SchemaRefinery/Modules/SchemaAnnotation
   SchemaRefinery/Modules/ApplyRecommendations

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

   SchemaRefinery/Tutorials/FullTutorial
   SchemaRefinery/Tutorials/DownloadAssembliesTutorial
   SchemaRefinery/Tutorials/AdaptLociTutorial
   SchemaRefinery/Tutorials/MatchSchemasTutorial
   SchemaRefinery/Tutorials/IdentifyParalogousLociTutorial
   SchemaRefinery/Tutorials/IdentifySpuriousGeneSchema
   SchemaRefinery/Tutorials/IdentifySpuriousGenesUnclassifiedCDS
   SchemaRefinery/Tutorials/SchemaAnnotationTutorial
   SchemaRefinery/Tutorials/ApplyRecommendationsTutorial


External Links:
---------------

**ChewBBACA Related Links:**

- `chewBBACA documentation <https://chewbbaca.readthedocs.io/en/latest/index.html>`_
- `chewBBACA GitHub repository <https://github.com/B-UMMI/chewBBACA>`_
- `ChewieNS documentation <https://chewie-ns.readthedocs.io/en/latest/>`_
- `ChewieNS website <https://chewbbaca.online>`_

**SchemaRefinery Related Links:**

- `NCBI datasets <https://www.ncbi.nlm.nih.gov/datasets/>`_
- `Python <https://www.python.org/>`_
- `Biopython <https://biopython.org/>`_
- `Requests <https://docs.python-requests.org/en/master/>`_
- `SchemaRefinery GitHub repository <https://github.com/B-UMMI/Schema_Refinery>`_