Metadata-Version: 2.4
Name: FinaleToolkit
Version: 0.11.1
Summary: FinaleToolkit is a package and standalone program to extract fragmentation features of cell-free DNA from paired-end sequencing data.
Author-email: James Li <lijw21@wfu.edu>, Ravi Bandaru <ravi.bandaru@northwestern.edu>, Yaping Liu <yaping@northwestern.edu>
License: MIT License
        
        Copyright (c) 2025 EpiFluidLab
        
        Permission is hereby granted, free of charge, to any person obtaining a copy
        of this software and associated documentation files (the "Software"), to deal
        in the Software without restriction, including without limitation the rights
        to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
        copies of the Software, and to permit persons to whom the Software is
        furnished to do so, subject to the following conditions:
        
        The above copyright notice and this permission notice shall be included in all
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        THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
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Project-URL: Homepage, https://epifluidlab.github.io/FinaleToolkit/
Project-URL: Repository, https://github.com/epifluidlab/finaletoolkit
Project-URL: Issues, https://github.com/epifluidlab/FinaleToolkit/issues
Project-URL: Changelog, https://github.com/epifluidlab/FinaleToolkit/blob/main/CHANGELOG.md
Project-URL: Wiki, https://github.com/epifluidlab/FinaleToolkit/wiki
Project-URL: Lab Website, https://epifluidlab.github.io/
Keywords: bioinformatics,cell free DNA,computational biology,genomics,epigenomics
Classifier: Programming Language :: Python :: 3
Classifier: License :: OSI Approved :: MIT License
Classifier: Operating System :: MacOS
Classifier: Operating System :: POSIX :: Linux
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Requires-Python: >=3.9
Description-Content-Type: text/markdown
License-File: LICENSE
Requires-Dist: numpy>=2
Requires-Dist: pysam
Requires-Dist: pybigwig
Requires-Dist: py2bit
Requires-Dist: tqdm
Requires-Dist: numba
Requires-Dist: scipy
Requires-Dist: pandas
Requires-Dist: statsmodels
Requires-Dist: loess
Requires-Dist: matplotlib
Dynamic: license-file

# <img alt="dna with letters FT" src="https://github.com/epifluidlab/FinaleToolkit/blob/b99b38e22a3b07ee9b7e0fa44a488a1eb5442efe/docs/_static/finaletoolkit_logo_rounded.png?raw=true" height="60"> ‎ ‎ ‎FinaleToolkit
<summary><h3>Table of Contents</h2></summary>
<ol>
  <li><a href="#about-the-project">About The Project</a></li>
  <li><a href="#installation">Installation</a></li>
  <li>
    <a href="#usage">Usage</a>
    <ul>
      <li><a href="#functionality">Functionality</a></li>
      <li><a href="#documentation">Documentation</a></li>
      <li><a href="#wikitutorials">Wiki/Tutorials</a></li>
      <li><a href="#compatible-file-formats">Compatible File Formats</a></li>
      <li><a href="#using-fragment-files">Using Fragment Files</a></li>
    </ul>
  </li>
  <li><a href="#contact">Contact</a></li>
  <li><a href="#license">License</a></li>
</ol>


## About The Project
FinaleToolkit (**F**ragmentat**I**o**N** **A**na**L**ysis of c**E**ll-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](https://img.shields.io/badge/DOI-10.1158%2F2159--8290.CD--19--0622-blue?style=flat-square&label=DOI)](https://doi.org/10.1158/2159-8290.cd-19-0622)
- Motif Diversity Score [![DOI](https://img.shields.io/badge/DOI-10.1158%2F2159--8290.CD--19--0622-blue?style=flat-square)](https://doi.org/10.1158/2159-8290.CD-19-0622)
- Windowed Protection Score [![DOI](https://img.shields.io/badge/DOI-110.1016%2Fj.cell.2015.11.050-blue?style=flat-square)](https://doi.org/10.1016/j.cell.2015.11.050)
- DELFI [![DOI](https://img.shields.io/badge/DOI-10.1038%2Fs41586--019--1272--6-blue?style=flat-square&link=https%3A%2F%2Fdoi.org%2F10.1038%252Fs41586-019-1272-6)](https://doi.org/10.1038%2Fs41586-019-1272-6)
- Cleavage Profile [![DOI](https://img.shields.io/badge/DOI-10.1073%2Fpnas.2209852119-blue?style=flat-square)](https://doi.org/10.1073/pnas.2209852119)

### Documentation
Documentation for FinaleToolkit can be found [here](https://epifluidlab.github.io/FinaleToolkit/).

### Wiki/Tutorials
The wiki and tutorial page for FinaleToolkit can be found [here](https://github.com/epifluidlab/FinaleToolkit/wiki).

### 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](http://finaledb.research.cchmc.org).

### Snakemake workflow

Check out our [Snakemake workflow](https://github.com/epifluidlab/finaletoolkit_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.
