Link to bioRxiv paper:
http://biorxiv.org/cgi/content/short/2023.04.25.537842v1?rss=1
Authors: Achouri, E., Felt, S. A., Hackbart, M., Lopez, C. B.
Abstract:
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.
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