CNV-BAC: Copy Number Variation Detection in Bacterial Circular Genome

Abstract

MotivationWhole genome sequencing (WGS) is widely used for copy number variation (CNV) detection. However, for most bacteria, their circular genome structure and high replication rate make reads more enriched near the replication origin. CNV detection based on read depth could be seriously influenced by such replication bias. ResultsWe show that the replication bias is widespread using ~200 bacterial WGS data. We develop CNV-BAC that can properly normalize the replication bias as well as other known biases in bacterial WGS data and can accurately detect CNVs. Simulation and real data analysis show that CNV-BAC achieves the best performance in CNV detection compared with available algorithms. Availability and implementationCNV-BAC is available at https://github.com/LinjieWu/CNV-BAC. Contactruibinxi@math.pku.edu.cn