Abstract
Bacterial viruses or (bacterio)phages recognize their microbial host, infect it, and convert the cell into a virus-producing machine within a matter of minutes. Classic RNA sequencing has become the method of choice to profile the transcriptional landscape of this infection process. However, short-read RNA sequencing approaches generally fail to capture key transcriptional features in dense viral genomes, such as operon structures and transcription start and stop sites. Taking advantage of the nanopore sequencing platform, we developed ONT-cappable-seq for end-to-end sequencing of primary prokaryotic transcripts to explore the dense and complex transcriptomes of phages and their bacterial hosts in unprecedented detail.

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