cfDNA-Flow
1. Overview
cfDNA-Flow facilitates the accurate and reproducible analysis of cfDNA WGS data. It offers various preprocessing options to accommodate different experimental setups and research needs in the field of liquid biopsies.
2. Preprocessing options
2.1 Trimming Options
cfDNA-Flow provides the flexibility to either trim or not trim the input reads based on the user's requirements. Trimming removes low-quality bases, which can impact downstream analyses.
2.2 Reference
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cfDNA UniFlow is a unified, standardized, and ready-to-use workflow for processing whole genome sequencing (WGS) cfDNA samples from liquid biopsies. It includes essential steps for pre-processing raw cfDNA samples, quality control and reporting. Additionally, several optional utility functions like GC bias correction and estimation of copy number state are included. Finally, we provide specialized methods for extracting coverage derived signals and visualizations comparing cases and controls. ...
