Currently, our diagnostic lab uses nanopore sequencing for virus detection. Sometimes, we are in the grey zone while assigning a specific virus species. Also, not all viruses are equally represented in the NCBI databases.
Other that the number of reads mapping to a viral genome, visualization on Jbrowse for the contigs and subsequent sequence similarity NCBI, what other metrices can I use to help them report these cases ?
Currently we are using Pavian for reporting ( https://ccb.jhu.edu/software/pavian/)