CfDNA UniFlow: a unified preprocessing pipeline for cell-free DNA data from liquid biopsies.

ABSTRACT:

Background

Cell-free DNA (cfDNA), a broadly applicable biomarker commonly sourced from urine or blood, is extensively used for research and diagnostic applications. In various settings, genetic and epigenetic information is derived from cfDNA. However, a unified framework for its processing is lacking, limiting the universal application of innovative analysis strategies and the joining of data sets.

Findings

Here, we describe cfDNA UniFlow, a unified, standardized, and ready-to-use workflow for processing cfDNA samples. The workflow is written in Snakemake and can be scaled from stand-alone computers to cluster environments. It includes methods for processing raw genome sequencing data as well as specialized approaches for correcting sequencing errors, filtering, and quality

SUBMITTER: Roner S 

PROVIDER: S-EPMC11659977 | biostudies-literature | 2024 Jan

REPOSITORIES: biostudies-literature