FinaleToolkit
Extract cell-free DNA fragmentation features from whole-genome sequencing, through one command line and Python API.
FinaleToolkit (FragmentatIoN AnaLysis of cEll-free DNA Toolkit) computes established cfDNA fragmentomic features (coverage, fragment length, WPS, DELFI, motifs, MDS, cleavage profiles) on a fast, streaming engine.
$ finaletoolkit coverage sample.bam intervals.bed -o coverage.bed
$ finaletoolkit wps sample.bam tss.bed --chrom-sizes hg38.chrom.sizes -o wps.bw -t 8
$ finaletoolkit end-motifs sample.bam hg38.2bit -k 4 -o motifs.tsv
import finaletoolkit as ftk
cov = ftk.coverage("sample.bam", "intervals.bed", output_file=None)
motifs = ftk.end_motifs("sample.bam", "hg38.2bit", k=4)
mds = motifs.motif_diversity_score()
Features¶
Fragment length
frag-length-binsfrag-length-intervals
Coverage
coverage
Windowed Protection Score
wpsadjust-wps
DELFI
delfi
End & breakpoint motifs
end-motifsbreakpoint-motifs
Motif Diversity Score
mdsregional-mds
Cleavage profile
cleavage-profile
Links¶
Citation¶
FinaleToolkit: Accelerating Cell-Free DNA Fragmentation Analysis with a High-Speed Computational Toolkit