tools-only Fragment Analysis - Usage Guide
Overview
Analyze cfDNA fragment size distributions and fragmentomics patterns for cancer detection. Extract nucleosome positioning signals and DELFI-style fragmentation profiles.
Prerequisites
# FinaleToolkit
pip install finaletoolkit
# Griffin (optional, for nucleosome profiling)
pip install griffin
# Dependencies
pip install pysam numpy pandas matplotlib
Quick Start
Tell your AI agent what you want to do:
- "Analyze fragment size distribution for tumor signal"
- "Calculate short-to-long fragment ratios across the genome"
- "Run DELFI-style fragmentomics analysis"
- "Profile nucleosome positioning from my cfDNA"
Example Prompts
Fragment Size Analysis
"Calculate the short (100-150bp) to long (151-220bp) fragment ratio for my sample."
"Generate genome-wide fragmentation profiles in 5Mb bins."
FinaleToolkit
"Run FinaleToolkit to replicate DELFI-style analysis."
"Calculate GC-corrected fragmentation ratios."
Nucleosome Profiling
"Analyze nucleosome accessibility around transcription start sites."
What the Agent Will Do
- Extract fragment sizes from BAM files
- Calculate short/long fragment ratios
- Generate genome-wide fragmentation profiles
- Apply GC correction if requested
- Compare patterns to healthy reference
Tips
- DELFI is a commercial company, NOT software - use FinaleToolkit (MIT license)
- FinaleToolkit 0.7.1+ is 50x faster than original DELFI approach
- Short fragments (100-150bp) are enriched in ctDNA
- Normal cfDNA peaks at ~167bp (mononucleosome)
- Griffin 0.2.0 is useful for tissue deconvolution
Related Skills
- cfdna-preprocessing - Preprocess before fragment analysis
- tumor-fraction-estimation - Complement with CNV-based estimation
- methylation-based-detection - Alternative detection approach