A benchmaking study on sub-genomic RNA landscape of Coronavirus by Nanopore sequencer

We used long reads sequencer, nanopore, look into the Bovine Coronavirus (BCoV) subgenomic RNA (sgRNA) landscape. Nanopore reads were basecalled by guppy and aligned by minimap2 with splice parameters. The sequenced RNA samples were extracted from the BCoV (U00735.2) infected HRT-18G cell lysate at 0.1 multiplicity of infection (MOI) and 48 hours post infection (hpi). The total RNA was extracted by TRIzol and the poly-(A) tail containing RNA was enriched by poly-d(T) beads.