A simplified pipeline for ctDNA sequencing data analysis

R package to work with ctDNA sequencing data

High-intensity sequencing reveals the sources of plasma circulating cell-free DNA variants

TNER: Tri-Nucleotide Error Reducer for ctDNA detection

MAGERI - Assemble, align and call variants for targeted genome re-sequencing with unique molecular identifiers

Deduplication for cfDNA sequencing data

Python package for cancer early detection based on a model of cancer evolution and circulating tumor DNA (ctDNA) shedding

A new CNV calling method for DNA-seq data

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

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.

Cancer estimation based on nucleosomes: Analysis of proportion of circulating tumor DNA fragments compared to nucleosome references.

Supplementary files for Paracchini, Beltrame et al., Clin Cancer Res, 2020.

Structural Variants in cell-free tumor DNA

Workflow for collapsing of standard binary alignment mapping file generated by MSK-ACCESS

Barcoded Molecular Families

Diagnostic performance of HPV-DeepSeek, a hybrid capture whole genome sequencing liquid biopsy for HPV-associated cancers

Workflow for making MSK-ACCESS standard binary alignment mapping file.

Extract read counts from cfDNA