| Name | FinaleToolkit JSON |
| Version |
0.11.0
JSON |
| download |
| home_page | None |
| Summary | FinaleToolkit is a package and standalone program to extract fragmentation features of cell-free DNA from paired-end sequencing data. |
| upload_time | 2025-09-05 22:18:19 |
| maintainer | None |
| docs_url | None |
| author | None |
| requires_python | >=3.9 |
| 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
copies or substantial portions of the Software.
THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
SOFTWARE.
|
| keywords |
bioinformatics
cell free dna
computational biology
genomics
epigenomics
|
| VCS |
 |
| bugtrack_url |
|
| requirements |
No requirements were recorded.
|
| Travis-CI |
No Travis.
|
| coveralls test coverage |
No coveralls.
|
# <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:
Li J*, Bandaru R*, Liu Y (2024) FinaleToolkit: Accelerating Cell-Free DNA Fragmentation Analysis with a High-Speed Computational Toolkit. BioRxiv Preprint [](https://doi.org/10.1101/2024.05.29.596414)
## Installation
You can 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 [](https://doi.org/10.1158/2159-8290.cd-19-0622)
- Motif Diversity Score [](https://doi.org/10.1158/2159-8290.CD-19-0622)
- Windowed Protection Score [](https://doi.org/10.1016/j.cell.2015.11.050)
- DELFI [](https://doi.org/10.1038%2Fs41586-019-1272-6)
- Cleavage Profile [](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).
## 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.
Raw data
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"description": "# <img alt=\"dna with letters FT\" src=\"https://github.com/epifluidlab/FinaleToolkit/blob/b99b38e22a3b07ee9b7e0fa44a488a1eb5442efe/docs/_static/finaletoolkit_logo_rounded.png?raw=true\" height=\"60\"> \u200e \u200e \u200eFinaleToolkit\n<summary><h3>Table of Contents</h2></summary>\n<ol>\n <li><a href=\"#about-the-project\">About The Project</a></li>\n <li><a href=\"#installation\">Installation</a></li>\n <li>\n <a href=\"#usage\">Usage</a>\n <ul>\n <li><a href=\"#functionality\">Functionality</a></li>\n <li><a href=\"#documentation\">Documentation</a></li>\n <li><a href=\"#wikitutorials\">Wiki/Tutorials</a></li>\n <li><a href=\"#compatible-file-formats\">Compatible File Formats</a></li>\n <li><a href=\"#using-fragment-files\">Using Fragment Files</a></li>\n </ul>\n </li>\n <li><a href=\"#contact\">Contact</a></li>\n <li><a href=\"#license\">License</a></li>\n</ol>\n\n\n\n\n## About The Project\nFinaleToolkit (**F**ragmentat**I**o**N** **A**na**L**ysis of c**E**ll-free DNA \n**Toolkit**) is a package and standalone program to extract fragmentation\nfeatures of cell-free DNA from paired-end sequencing data.\n\n### Citation\nIf you use FinaleToolkit in your research, please consider citing our paper:\n\nLi J*, Bandaru R*, Liu Y (2024) FinaleToolkit: Accelerating Cell-Free DNA Fragmentation Analysis with a High-Speed Computational Toolkit. BioRxiv Preprint [](https://doi.org/10.1101/2024.05.29.596414)\n\n\n## Installation\nYou can install the package using `pip`.\n```\n$ pip install finaletoolkit\n```\n\n## Usage\n\n### Functionality\n\nFinaleToolkit has support for the following cell-free DNA fragmentation features:\n\n- Fragment Length\n- Coverage\n- End Motifs [](https://doi.org/10.1158/2159-8290.cd-19-0622)\n- Motif Diversity Score [](https://doi.org/10.1158/2159-8290.CD-19-0622)\n- Windowed Protection Score [](https://doi.org/10.1016/j.cell.2015.11.050)\n- DELFI [](https://doi.org/10.1038%2Fs41586-019-1272-6)\n- Cleavage Profile [](https://doi.org/10.1073/pnas.2209852119)\n\n### Documentation\nDocumentation for FinaleToolkit can be found [here](https://epifluidlab.github.io/FinaleToolkit/).\n\n### Wiki/Tutorials\nThe wiki and tutorial page for FinaleToolkit can be found [here](https://github.com/epifluidlab/FinaleToolkit/wiki).\n\n### Compatible File Formats\n\nFinaleToolkit is compatible with almost any paired-end sequence data:\n\n- Binary Alignment Map (`.bam`) files with an associated index file (`.bam.bai`).\n- Compressed Reference-oriented Alignment Map (`.cram`) files.\n- Fragment (`.frag.gz`) files with an associated tabix index file (`.frag.gz.tbi`).\n\n### Using Fragment Files\n\nFragment (`.frag.gz`) files are block-gzipped BED3+2 files with the following columns: `chrom` , `start` , `stop` , `mapq` , `strand`.\n\nWe encourage you to use our comprehensive database, FinaleDB, to access relevant fragment files. Learn more about FinaleDB [here](http://finaledb.research.cchmc.org).\n\n## Contact\n- James Li: lijw21@wfu.edu\n- Ravi Bandaru: ravi.bandaru@northwestern.edu\n- Yaping Liu: yaping@northwestern.edu\n\n## License\nThis project falls under an MIT license. See the included `LICENSE` file for details.\n",
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