FinaleToolkit is a package and standalone program to extract fragmentation features of cell-free DNA from paired-end sequencing data.
Project description
FinaleToolkit
Table of Contents
About The Project
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.
Citation
If you use FinaleToolkit in your research, please consider citing our paper:
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
- Motif Diversity Score
- Windowed Protection Score
- DELFI
- Cleavage Profile
Documentation
Documentation for FinaleToolkit can be found here.
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
). - Sequence Alignment Map (
.sam
) files. - 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.
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.
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