vConTACT3 Documentation
=======================

Welcome to the documentation for **vConTACT3** — a viral genome clustering and taxonomic assignment tool.

vConTACT3 is the latest iteration in the vConTACT family. Each version improves upon the foundational philosophy: more
related virus genomes should share more genes - **V**\ iral **CONT**\ ig **A**\ utomatic **C**\ lustering and **T**\ axonomy.

vConTACT3 is faster, more scalable, more accurate, and features more outputs than prior versions. Databases are now handled
more efficiently and are more portable than before.

Contents:
---------

.. toctree::
   :maxdepth: 1
   :caption: User Guide

   installation
   quickstart
   cli/index
   examples
   troubleshooting

.. toctree::
   :maxdepth: 1
   :caption: Inputs & Outputs

   inputs_parameters
   results
   prediction_file
   exports

.. toctree::
   :maxdepth: 1
   :caption: Databases

   databases

.. toctree::
   :maxdepth: 1
   :caption: Performance & Optimization

   memory_usage

.. toctree::
   :maxdepth: 1
   :caption: About & Citations

   citations
   release_notes