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.
If you use FinaleToolkit in your research, please consider citing our paper:
You can install the package using pip.
$ 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 found here.
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).
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.
- 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 included LICENSE file for details.
