‎ ‎ ‎FinaleToolkit

Table of Contents

1. About The Project
2. Installation
3. Usage
   • Functionality
   • Documentation
   • Wiki/Tutorials
   • Compatible File Formats
   • Using Fragment Files
4. Contact
5. License

About The Project

FinaleToolkit (FragmentatIoN AnaLysis of cEll-free DNA Toolkit) is a package and standalone program to extract fragmentation features of cell-free DNA from paired-end sequencing data.

Citation

If you use FinaleToolkit in your research, please consider citing our paper:

James Wenhan Li, Ravi Bandaru, Kundan Baliga, Yaping Liu, FinaleToolkit: Accelerating Cell-Free DNA Fragmentation Analysis with a High-Speed Computational Toolkit, Bioinformatics Advances, 2025;, vbaf236, https://doi.org/10.1093/bioadv/vbaf236

Installation

You can install the package using conda.

$ conda install -c bioconda -c conda-forge finaletoolkit

You can also install the package using pip.

$ pip install finaletoolkit

Usage

Functionality

FinaleToolkit has support for the following cell-free DNA fragmentation features:

• Fragment Length
• Coverage
• End Motifs
• Motif Diversity Score
• Windowed Protection Score
• DELFI
• Cleavage Profile

Documentation

Documentation for FinaleToolkit can be found here.

Wiki/Tutorials

The wiki and tutorial page for FinaleToolkit can be found here.

Compatible File Formats

FinaleToolkit is compatible with almost any paired-end sequence data:

• Binary Alignment Map (.bam) files with an associated index file (.bam.bai).
• Compressed Reference-oriented Alignment Map (.cram) files.
• Fragment (.frag.gz) files with an associated tabix index file (.frag.gz.tbi).

Using Fragment Files

Fragment (.frag.gz) files are block-gzipped BED3+2 files with the following columns: chrom , start , stop , mapq , strand.

We encourage you to use our comprehensive database, FinaleDB, to access relevant fragment files. Learn more about FinaleDB here.

Snakemake workflow

Check out our Snakemake workflow!

Contact

• James Li: lijw21@wfu.edu
• Ravi Bandaru: ravi.bandaru@northwestern.edu
• Yaping Liu: yaping@northwestern.edu

License

This project falls under an MIT license. See the included LICENSE file for details.