FinaleToolkit
Table of Contents
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.
1 maintainer
Metadata
1 maintainer
Release files for FinaleToolkit 1.1.0
For a detailed explanation of source distributions (sdists) and built distributions (wheels), please see the package formats documentation.
Source distribution (sdist)
| File | Size | Uploaded | |
|---|---|---|---|
| finaletoolkit-1.1.0.tar.gz | 134.1 kB | Details |
Built distribution (wheel)
| File | Interpreter | ABI | Platform | Reset |
|---|---|---|---|---|
| finaletoolkit-1.1.0-py3-none-any.whl | Python 3 | none | any | Details |
Total release size: 250.3 kB
Release files / finaletoolkit-1.1.0.tar.gz
| Download URL | finaletoolkit-1.1.0.tar.gz |
|---|---|
| Size | 134.1 kB |
| Tags | Source |
|
SHA-256 checksum How to use checksums |
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Transparency logRelease files / finaletoolkit-1.1.0-py3-none-any.whl
| Download URL | finaletoolkit-1.1.0-py3-none-any.whl |
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| Size | 116.2 kB |
| Tags | Python 3 |
|
SHA-256 checksum How to use checksums |
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Uploaded using Trusted Publishing? What is trusted publishing? |
Yes |
| Uploaded via |
twine/6.1.0 CPython/3.13.14
|
Provenance
Provenance describes where a file came from. On PyPI, provenance is shared via attestations, which provide a verifiable record of the build or publishing details. View details, limitations and caveats.
PyPI Publish Attestation
PyPI verified that this artifact, at this checksum, originated from the publisher listed below.
Signed by GitHub Actions, verified by PyPI on Jul 23, 2026.
Transparency log
