CAPELLINI
=========

**CRISPR-Abundance Phage-Evidence Linkage for Leveraging Interaction
Network Inference**

.. image:: ../_static/logo.png
   :alt: CAPELLINI logo
   :align: center
   :width: 320px

CAPELLINI is an integrative method for inferring phage–host interactions
from paired 16S rRNA amplicon and viral metagenomics data. It combines
**dataset-specific CRISPR evidence** with **abundance-based statistical
network inference**.

.. toctree::
   :maxdepth: 2
   :caption: User guide

   installation
   quickstart
   pipeline
   configuration

.. toctree::
   :maxdepth: 2
   :caption: Reference

   api

.. toctree::
   :maxdepth: 1
   :caption: About

   citation


Indices
-------

* :ref:`genindex`
* :ref:`modindex`
* :ref:`search`