DNAvi - Integration, statistics and visualization of cfDNA fragment traces

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.

Contents

• Installation
• Quickstart
• Inputs
• Ladders (DNA size standards)
• Metadata
• Nucleosomal fractions
• Normalization
• Outputs
• Visualization
• Statistics
• Biological Interpretation
• Advanced Settings
• API Reference

Workflow

Quickstart

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

Violin plots for average nucleosomal fractions including statistics

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.