Identifying Multipartite viruses (Viral Bioinformatics)

Question

[pixie@bioinfo]

Hello, we currently perform virus detection using Nanopore pipeline in plants. We do a quick reference-based detection and not de novo. We often visualize the best hits on Jbrowse for a final conclusion about the coverage, apart from the read depth and length of the reads.

1. In this setting, is it possible to identify multipartite viruses having more than one genome segment ?

1. Is it possible to identify the contigs from the bam files ? I could get only the consensus sequence based on the reference.

It will be great if I could run some command line tools which will not take days to run.

Thanks.