.. _api_generate_hic:

============================
Generate Hi-C matrices (API)
============================

In :ref:`generate_hic` we built a Hi-C matrix from FASTQ using command line tools, either
with ``fanc auto`` or using :ref:`fanc-modular`. Here, we will accomplish the same using
only the Python API.

.. toctree::
   :maxdepth: 1

   Mapping FASTQ files <generate/map>
   Generating and filtering ReadPairs <generate/pairs>
   Generating, binning, and filtering Hic objects <generate/hic>