Carbapenemase-encoding gene Copy Number Estimator (CCNE) is a ready-to-use bioinformatics tool that was developed to estimate blaCarb copy number from whole genome sequencing data. CCNE has two components, CCNE-acc and CCNE-fast. CCNE-acc detected blaCarb copy number in a comprehensive and high accuracy way, while CCNE-fast was designed for rapid screening of blaCarb copy numbers.