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DNAvi -  Integration, statistics and visualization of cfDNA fragment traces
===================

.. image:: _static/logo.jpg
    :width: 80
    :alt: logo

DNAvi is a Python-based tool for rapid analysis and visualization of cell-free DNA (cfDNA) fragment size profiles directly from electrophoresis data, without the need for sequencing. It enables normalization, statistical comparison, and publication-ready plotting of multiple samples, supporting quality control and exploratory fragmentomics in clinical and research workflows.


.. toctree::
   Installation
   Quickstart
   Inputs
   Ladders
   Metadata
   NucleosomalFractions
   Normalization
   Outputs
   Visualization
   Statistics
   Biology
   Advanced
   :maxdepth: 1
   :caption: Contents



Workflow
^^^^^^^^^^^^^^^^^^

.. image:: _static/workflow.png
    :width: 600
    :alt: workflow


Quickstart
^^^^^^^^^^^^^^^^^^

.. code-block::

    python3 DNAvi.py -i tests/electropherogram.csv -l tests/ladder.csv -m tests/metadata.csv


Example output
^^^^^^^^^^^^^^^^^^

Cell-free DNA electropherogram similarity clustering with group annotation

.. image:: _static/example_cluster_condition.jpg
    :width: 600
    :alt: workflow

Violin plots for average nucleosomal fractions including statistics

.. image:: _static/example_stats_violin.png
    :width: 600
    :alt: stats

Citation
^^^^^^^^^^^^^^^^^^

Please cite DNAvi as:

Hess, A., Seelow, D. & Kretzmer, H. DNAvi: Integration, statistics, and visualization of cell-free DNA fragment traces. *Bioinformatics* (2026) doi:10.1093/bioinformatics/btag041.