.. cfDNApipe documentation master file, created by
   sphinx-quickstart on Tue Jan  5 09:27:23 2021.
   You can adapt this file completely to your liking, but it should at least
   contain the root `toctree` directive.

Welcome to cfDNApipe's documentation!
=====================================

.. toctree::
   :maxdepth: 2
   :hidden:
   :caption: Contents:

   Up-Down-Stream-Flowchart
   Basic-Data-Processing
   Quality-Control
   Methylation-Analysis
   Large-Scale-CNV
   Bin-Scale-CNV
   Fragmentomics
   Virus-Detection
   SNV-Detection



**cfDNApipe(cell free DNA Pipeline)** is an integrated pipeline for
analyzing `cell-free DNA`_ WGBS/WGS data. It contains many cfDNA quality
control and feature extration algorithms. Also we collected some useful
cell free DNA references and provide them `here`_.

The whole pipeline was established based on processing graph principle.
Users can use the inside integrated pipeline for WGBS/WGS data as well
as build their own analysis pipeline from any intermediate data like bam
files. The main functions are as the following picture.

.. figure:: ./pics/pipeline.png

   cfDNApipe Functions 


cfDNApipe Analysis Workflow
~~~~~~~~~~~~~~~~~~~~~~~~~~~

.. figure:: ./pics/cfDNApipe_flowchart.png

   cfDNApipe Workflow Overview


.. _cell-free DNA: https://en.wikipedia.org/wiki/Circulating_free_DNA
.. _here: https://honchkrow.github.io/cfDNAReferences/


Indices and tables
==================

* :ref:`search`