This workflow is runs FinaleToolKit (FragmentatIoN AnaLysis of cell-free DNA Toolkit) under the hood, a standalone python-based package for fragmentomics analysis of paired-end cfDNA sequencing data from platforms WGS, WGBS and ChIP. The pipeline has been tested with sorted and indexed bam as input. Fragmentation features extracted include fragment length, covarage, end motifs, motif diversity score (MDS), window protection score (WPS), DELFI (ratio of GC corrected short to long fragment) score and cleavage profile.
Requires: Python version > 3.8, snakemake>7.0, singularity