cfDNAlab documentation

Welcome to the user documentation for cfDNAlab.

cfDNAlab contains a set of ultra-fast command-line tools for analysis of cell-free DNA. They allow you to extract fragment coverage, midpoint coverage, fragment end- and breakpoint motifs, and fragment lengths across the whole genome (or in windows) in mere seconds or minutes.

The commands are specifically optimized for WGS cfDNA and work directly on cfDNA fragments from either paired-end sequencing data or unpaired data where each read represents a full fragment.

To accommodate for common biases, all commands allow sample-specific GC correction and large-scale genomic smoothing (when local changes should not be overshadowed by global differences).

The commands are highly flexible with many options and good default settings. See Guides in the menu for examples.

Use the Get Started section for installation, common input files, and first commands.

Use CLI Reference for command help pages.