FinaleToolkit

About

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: epifluidlab/finaletoolkit

• Bug reports: epifluidlab/finaletoolkit#issues

Documentation

• FinaleToolkit Documentation
  • User Guide
  • CLI
  • API
• User Guide
  • Introduction
  • Input Data
  • Features
  • Installation
  • Structure
  • Intersect Policy
  • Quickstart
  • Help
• CLI
  • Named Arguments
  • Sub-commands
• API
  • Basic Features
  • Window Protection Score (WPS)
  • DELFI
  • End-Motifs
  • Cleavage Profile
  • Frag File Utilities
  • Genome Utilities

Citations

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
}

Contact

James Wenhan Li

Email: lijw21@wfu.edu

Ravi Bandaru

Email: ravi.bandaru@northwestern.edu

Yaping Liu

Email: yaping@northwestern.edu

License

For academic research, please refer to MIT license.