FinaleToolkit logo  FinaleToolkit

Docs DOI License: MIT

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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 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!

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

License

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

Project links

Data verified by PyPI on Jul 23, 2026
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Key dates

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  • Released:
Latest release

1 maintainer

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Avatar for jli124 from gravatar.com jli124

Credits

Author: James Li

GitHub Statistics

Data verified by PyPI on Jul 23, 2026
The GitHub source repository was provided by the project maintainers and verified by PyPI at the time of upload. Stars, forks, and open issues/PRs are derived from that repository and have not been independently verified.

License

MIT License (MIT License)

Requires

Python >=3.10

Tags

bioinformatics cell free DNA computational biology genomics epigenomics

Classifiers

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