Figure 1. SSV-Seq 2.0 workflow. The SSV-Seq protocol was described in Lecomte et al. (Lecomte et al., 2019) (left panel). The optimized SSV-Seq 2.0 protocol is represented on the right side. A total quantity of 8x1011 vector genomes of purified rAAV vector sample is required as input. A pretreatment with a DNases cocktail can be performed prior to DNA extraction to specifically identify and quantify DNA that are encapsidated in rAAV capsids. A second strand synthesis step is carried out, followed by the PCR-free DNA library preparation. Finally, high-throughput sequencing is performed using Illumina HiSeq platform (rapid run 2x94 pb).