Optimizing RNA-Seq strategies for transcriptomic analysis of complex viral genomes

Transcriptome profiling has become routine in studies of many biological processes. However, favored approaches such as short-read Illumina RNA sequencing are giving way to long-read sequencing platforms better suited to interrogating the complex transcriptomes typical of many RNA and DNA viruses. Here, researchers from the New York University School of Medicine provide a guide – tailored to molecular virologists – to the ins-and-outs of viral transcriptome sequencing and discuss the strengths and weaknesses of the major RNA sequencing technologies as tools to analyze the abundance and diversity of viral transcripts made during infection.