Introduction

Circulating cell-free DNA (cfDNA) refers to highly fragmented DNA that circulate in blood plasma. In healthy conditions, cfDNA mainly originates from hematopoietic cells through apoptosis or necrosis. In pathological states, additional cfDNA is released from the genomes of otherwise inaccessible tissues (e.g., from tumors in cancer).

CfDNA fragmentation patterns have been established as a promising non-invasive biomarker for disease detection and monitoring. It has been shown that fragmentation pattern and cfDNA tissue-of-origin changes are associated with changes in different pathological statuses.

Computational approaches can extract fragmentation features from cfDNA whole genome sequencing (WGS) data. However, various established cfDNA fragmentation features (ex. Windowed Protection Score (WPS), Motif Diversity Score (MDS), DELFI) have source code which is often absent, poorly documented, ad hoc, and unmaintained.

FinaleToolkit offers a solution to this. It is a fast and comprehensive toolkit that provides a user-friendly interface to extract various cfDNA fragmentation features from fragmentation data. It is designed to be easy to use, well-documented, and maintained.