FinaleToolkit
=========================================

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About
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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.

- **Website:** https://epifluidlab.github.io/finaletoolkit-docs/
- **PyPI:** https://pypi.org/project/finaletoolkit/
- **Documentation:** https://epifluidlab.github.io/finaletoolkit-docs/documentation
- **Source code:** https://github.com/epifluidlab/finaletoolkit
- **Bug reports:** https://github.com/epifluidlab/finaletoolkit/issues


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Documentation
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.. toctree::
   :maxdepth: 2
   
   documentation/index
   documentation/user_guide/index
   documentation/cli_reference/index
   documentation/api_reference/index
   
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Citations
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If FinaleToolkit is integral to a scientific publication, please cite it. A paper describing FinaleToolkit has been written. Here is a ready-made BibTeX entry::

    @article{
    Li JW, Bandaru R, Liu Y. FinaleToolkit: Accelerating Cell-Free DNA Fragmentation Analysis with a High-Speed Computational Toolkit. Preprint. bioRxiv. 2024;2024.05.29.596414. Published 2024 Jun 2. doi:10.1101/2024.05.29.596414
    }

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Contact
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| **James Wenhan Li**
| Email: lijw21@wfu.edu

| **Ravi Bandaru**
| Email: ravi.bandaru@northwestern.edu

| **Yaping Liu**
| Email: yaping@northwestern.edu

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License
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For academic research, please refer to MIT license.