seqCNA

seqCNA is a parallelized R package to enhance copy number analysis in cancer research using high-throughput sequencing data. The tool addresses the challenges of accurately detecting copy number alterations (CNAs) and structural rearrangements in the genome that play a critical role in tumorigenesis by affecting gene expression patterns. Understanding CNAs is crucial for understanding cancer discrimination, progression, and complexity.

SeqCNA introduces new techniques to improve the accuracy of CNA (Copy number alteration) profiles. These methods involve filtering to reduce the number of false positives and correcting for GC (guanine-cytosine) content bias, which significantly impacts the quality of copy number profiles, mainly when there is high read coverage and a strong correlation between GC content and copy number. The package is designed to automatically select appropriate analysis steps based on the availability of paired-end mapping, matched normal samples, and genome annotation, facilitating a streamlined and efficient analysis workflow.