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fragment-analysis

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Extracts cfDNA fragmentomics features (DELFI genome-wide short/long ratios, WPS nucleosome positioning, Griffin GC-corrected accessibility profiles, end-motifs/MDS, OCF) for cancer detection and tissue-of-origin from plasma WGS. Centers on the nuclease-footprint reframe (every feature re-reads one nucleosome object), the mandatory GC correction, and the cross-protocol non-comparability that breaks naive classifiers. Runs FinaleToolkit (real CLI/Python, MIT) and the Griffin Snakemake pipeline; DELFI is a method, not a package. Use when deriving fragment-based signal from cfDNA, choosing a feature family for detection vs subtyping, or diagnosing why a fragmentomic model failed validation.

When to use

• Deriving fragment-based signal from cfDNA
• Choosing a feature family for detection vs subtyping
• Diagnosing why a fragmentomic model failed validation
• Quantifying nucleosome-footprint features
• Running FinaleToolkit
• Running the Griffin Snakemake pipeline
• Calculating custom binned short/long ratio

When not to use

• Using DELFI as a pip install-able tool
• Importing Griffin as a function

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