In this short review, we highlight the importance of combining cell culture and nextgeneration sequencing for the study of viruses in aquaculture. Moreover, we summarize some key examples of previously published studies that have implemented this approach and discuss the advantages of nanopore sequencing and other long-read sequencing technologies. With the rapid advances of genomic research, selection of the best tool to carry out analyses, it's a computational challenge, but the potential for their applications is enormous. Therefore, this mini-review highlights important NGS bioinformatic tools and recent studies in cell culture for the study of aquatic virology.