FinaleToolkit

Table of Contents

• About The Project
• Installation
• Usage
  • Functionality
  • Documentation
  • Wiki / Tutorials
  • Compatible File Formats
  • Using Fragment Files
  • Snakemake Workflow
• Contributing
• Contact
• 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

Install with conda:

conda install -c bioconda -c conda-forge finaletoolkit

Or with pip:

pip install finaletoolkit

Usage

Functionality

FinaleToolkit supports 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!

Contributing

PRs that change src/finaletoolkit/ should add a CHANGELOG.md entry under [Unreleased]. See RELEASING.md for that convention and for how releases are cut.

Contact

• James Li: james.li3@northwestern.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.