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.

Ultra-fast command line tools for extracting bias-corrected fragmentation patterns from 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.

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.

Code and workflows for the cfMeDIP‑seq Data Resource: end‑to‑end methylation & fragmentomic feature extraction, PCA, and machine‑learning classifiers (cancer vs normal, cancer type & subtype) from Zeng and Abelman et al. (2026)

A pipeline analyzing fragmentomics profile of cfDNA sequencing data

Fragmentomics analysis of cfDNA using WGS: alignment, fragment-length profiling, end-motif analysis, healthy vs cancer comparisons, and biomarker discovery.