VODKA2: An accurate method to detect copy-back and deletion viral genomes from next-generation sequencing data

During viral replication, RNA viruses produce non-standard viral genomes (nsVGs), including copy-back viral genomes (cbVGs) and deletion viral genomes (delVGs), that play a crucial role in regulating viral replication. The sequences of these nsVGs are highly similar to the standard genome, making identification and quantification of the species generated during viral infections a challenging task. Here, we present our next-generation sequencing data analysis pipeline, Viral Opensource DVG Key Algorithm 2 (VODKA2), that identifies nsVGs with high accuracy from NGS data. ### Competing Interest Statement The authors have declared no competing interest.