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Quick Start
Getting started with FinaleToolkit is fairly simple:
- (Optional) Create and activate a
condaenvironment with a Python version greater than 3.8
conda create --name FTK python=3.11
conda activate FTK- Install the package using
pip.
pip install finaletoolkit- Run
finaletoolkit --helpin your command-line interface. Your output should look like this:
Usage: finaletoolkit [OPTIONS] COMMAND [ARGS]...
A package and standalone program to extract fragmentation features of cell-free
DNA from paired-end sequencing data. Run a subcommand with --help to see its
options and an example invocation. For file outputs, pass "-o -" to write to
standard output instead of a file.
╭─ Options ────────────────────────────────────────────────────────────────────────╮
│ ╭──────────┬────┬──────────────────────────────────────────────────────────────╮ │
│ │--version │ -v │ Show the version and exit. │ │
│ │--help │ -h │ Show this message and exit. │ │
│ ╰──────────┴────┴──────────────────────────────────────────────────────────────╯ │
╰──────────────────────────────────────────────────────────────────────────────────╯
╭─ Coverage & Fragment Length ─────────────────────────────────────────────────────╮
│ coverage Fragmentation coverage over BED intervals from a │
│ BAM/CRAM/Fragment file. │
│ frag-length-bins Fragment lengths grouped into bins from a │
│ BAM/CRAM/Fragment file. │
│ frag-length-intervals Fragment-length summary statistics over BED intervals. │
╰──────────────────────────────────────────────────────────────────────────────────╯
╭─ Protection & Cleavage ──────────────────────────────────────────────────────────╮
│ wps Windowed Protection Score (WPS) over BED sites. │
│ adjust-wps Adjust raw WPS with a median filter and a Savitsky-Golay │
│ filter. │
│ cleavage-profile Cleavage proportion over BED intervals from a │
│ BAM/CRAM/Fragment file. │
╰──────────────────────────────────────────────────────────────────────────────────╯
╭─ DELFI ──────────────────────────────────────────────────────────────────────────╮
│ delfi DELFI features: short/long fragments, DELFI ratio, and total fragments. │
╰──────────────────────────────────────────────────────────────────────────────────╯
╭─ Motifs & MDS ───────────────────────────────────────────────────────────────────╮
│ end-motifs Frequency of k-mer 5' end motifs. │
│ interval-end-motifs Frequency of k-mer 5' end motifs in each region │
│ of a BED file. │
│ breakpoint-motifs Frequency of k-mer breakpoint motifs. │
│ interval-breakpoint-motifs Frequency of k-mer breakpoint motifs in each │
│ region of a BED file. │
│ mds Motif diversity score (MDS) from k-mer │
│ frequencies (Jiang et al., 2020). │
│ regional-mds Regional Motif Diversity Score (rMDS) for each │
│ region (Bandaru et al. 2026). │
╰──────────────────────────────────────────────────────────────────────────────────╯
╭─ Utilities ──────────────────────────────────────────────────────────────────────╮
│ filter-file Filter a BED/BAM/CRAM file by pairing, MAPQ, flags, length, and │
│ regions. │
│ agg-bw Aggregate a bigWig signal over constant-length BED intervals. │
│ gap-bed BED4 of centromeres, telomeres, and short-arm intervals (UCSC │
│ hg19 gaps). │
╰──────────────────────────────────────────────────────────────────────────────────╯
FinaleToolkit