QDNAseq

QDNAseq is a software pipeline to enhance the detection of DNA copy number aberrations using shallow whole-genome sequencing (WGS), particularly in challenging samples such as formalin-fixed paraffin-embedded (FFPE) archival material commonly used in cancer studies. This method addresses numerous obstacles inherent to DNA copy number analysis, including imperfections in the human reference genome, repetitive sequences and polymorphisms, variability in sample quality, and biases introduced during sequencing processes.

QDNAseq distinguishes itself by implementing a dual correction strategy that accounts for sequence mappability and GC content, significantly improving upon previous methodologies. Moreover, it utilizes sequence data from the 1000 Genomes Project to develop a comprehensive blacklist of problematic genome regions, most of which were previously unrecognized, thus allowing for more accurate copy number analysis.