FinaleToolkit: accelerating cell-free DNA fragmentation analysis with a high-speed computational toolkit.

ABSTRACT:

Motivation

Cell-free DNA (cfDNA) fragmentation pattern represents a promising non-invasive biomarker for disease diagnosis and prognosis. Numerous fragmentation features, such as end motif and window protection score (WPS), have been characterized in cfDNA genomic sequencing. However, the analytical tools developed in these studies are often not released to the liquid biopsy community or are inefficient for genome-wide analysis in large datasets.

Results

To address this gap, we have developed FinaleToolkit, a fast and memory-efficient Python package designed to generate comprehensive fragmentation features from large cfDNA genomic sequencing data. For instance, FinaleToolkit can generate genome-wide WPS features from a ∼100× cfDNA whole-genome sequencing (WGS) dataset with o

SUBMITTER: Li JW 

PROVIDER: S-EPMC12597888 | biostudies-literature | 2025

REPOSITORIES: biostudies-literature