Repository files navigation

1. About The Project
2. Installation
3. Usage
   • Functionality
   • Documentation
   • Wiki/Tutorials
   • Compatible File Formats
   • Using Fragment Files
4. Contact
5. License

FinaleToolkit (FragmentatIoNAnaLysis of cEll-free DNAToolkit) is a package and standalone program to extract fragmentationfeatures of cell-free DNA from paired-end sequencing data.

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

You can install the package usingpip.

$ pip install finaletoolkit

FinaleToolkit has support for the following cell-free DNA fragmentation features:

• Fragment Length
• Coverage
• End Motifs
• Motif Diversity Score
• Windowed Protection Score
• DELFI
• Cleavage Profile

Documentation for FinaleToolkit can be foundhere.

The wiki and tutorial page for FinaleToolkit can be foundhere.

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).

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 FinaleDBhere.

• James Li:lijw21@wfu.edu
• Ravi Bandaru:ravi.bandaru@northwestern.edu
• Yaping Liu:yaping@northwestern.edu

This project falls under an MIT license. See the includedLICENSE file for details.