We developed an integrated workflow combining long-read sequencing and multiplex dPCR for comprehensive characterization of rAAV vectors. 

We assessed vector genome integrity, purity, size distribution, and sequence identity within an rAAV9 batch. 

Long-read sequencing identified a predominantly full-length vector population with a small proportion of truncated genome fragments. 

Multiplex dPCR provided absolute quantification of genome configurations and confirmed sequencing results as an orthogonal method. 

The combined approach delivers a robust, high-confidence evaluation of rAAV quality, supporting gene therapy development, safety assessment, and lot release testing.