Dear Guillermo

Nonsegmented RNA follows a sequential pattern of gene expression. With segmented RNA, each individual segment is contained in a distinct RNP complex. These complexes function independently of transcription and replication related processes.

Dear Guillermo

Nonsegmented RNA follows a sequential pattern of gene expression. With segmented RNA, each individual segment is contained in a distinct RNP complex. These complexes function independently of transcription and replication related processes.

https://academic.oup.com/bioinformatics/article/30/13/1793/2422158

It use Diamond to align de novo assembled transcript (eg: Trinity results) to the trEMBL database and then select those transcripts that mapped to Virus proteins using the annotation data provided by UniProt.

In a metagenomic analysis I would recommend you to align de novo your reads (e.g metaspades )Article MetaSPAdes: A new versatile metagenomic assembler

and then maybe use prokka to annotate and recognize virus sequences

Article Prokka: Rapid prokaryotic genome annotation

or also to classify with Kraken as it has a database for viruses also.

Article Wood DE, Salzberg SL.. Kraken: Ultrafast metagenomic sequenc...

with this options you could get an overall idea about the virus sequences in your sample.