Welcome to Nanomotif's documentation!
===================================

**Nanomotif** is a Python package designed to explore methylation in prokaryotic genomes
using Nanopore sequencing. Nanomotif is a fast, scalable, and sensitive tool for identification and utilization 
of methylation motifs in monocultures and metagenomic samples. Nanomotif offers de novo methylated motif identification, 
metagenomic bin contamination detection, bin association of unbinned contigs, and linking of MTase genes to methylation motifs.


Check out the :doc:`usage` section for further information, including
how to :ref:`installation` the project.

.. note::

   This project is under active development.


.. toctree::
   installation
   required_files
   usage
   output
   examples
   known_issues
   troubleshooting