FinaleToolkit is a package and standalone program to extract fragmentation features of cell-free DNA from paired-end sequencing data.

LIONHEART detects cancer from whole genome sequenced plasma cell-free DNA.

As a cell-free DNA (cfDNA) processing pipeline, Triton conducts fragmentomic and phased-nucleosome coverage analyses on individual or composite genomic regions and outputs both region-level biomarkers and nt-resolution signal profiles.

A pipeline analyzing fragmentomics profile of cfDNA sequencing data

Raw signals were basecalled with Dorado and aligned to hg38.p13 using minimap2. Tumor fraction and CNVs were estimated with HMMcopy and ichorCNA. Motif analysis extracted the first four 5′ nucleotides per read, and NMF identified three dominant motif profiles capturing key variability among samples.

Raw signals were basecalled with Dorado and aligned to hg38.p13 using minimap2. Tumor fraction and CNVs were estimated with HMMcopy and ichorCNA. Motif analysis extracted the first four 5′ nucleotides per read, and NMF identified three dominant motif profiles capturing key variability among samples.