Estimating tumor fraction in cell-free DNA from ultra-low-pass whole genome sequencing.

Copy number calling and variant classification using targeted short read sequencing

cfDNApipe: A comprehensive quality control and analysis pipeline for cell-free DNA high-throughput sequencing data

R package to work with ctDNA sequencing data

cfDNAPro specializes in standardized and robust cfDNA fragmentomic analysis

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

Bayesian-based fetal genotyping using maternal cell-free DNA and parental sequencing data.

An awesome set of epigenetic pipelines for bulk cfChip-seq, ChIP-seq, and ATAC-seq

As a tool for cancer subtype prediction, Keraon uses features derived from cell-free DNA (cfDNA) in conjunction with PDX reference models to perform both classification and heterogenous phenotype fraction estimation.

Pipeline to call SNV's with 4 tools (VarDict, LoFreq, Mutect2 & SiNVICT)

cell-free ChIP-seq pipeline

Extract read counts from cfDNA

Hunting for CMV and HHV-6 in cfDNA sequence

A code to simulate the events of cell-free protein expression

Structural Variants in cell-free tumor DNA