‎ ‎ ‎FinaleToolkit

May 26, 2026 · View on GitHub

Table of Contents
  1. About The Project
  2. Installation
  3. Usage
  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 DOI
  • Motif Diversity Score DOI
  • Windowed Protection Score DOI
  • DELFI DOI
  • Cleavage Profile DOI

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

License

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