SSU from single genomes

[timyerg]

Hello!
Thank you for the tool.
I have shotgun data from single isolates and assembled genomes (SPAdes for isolates). My goal was to extract rRNA from assembled genomes, but now I saw this tool and wonder if this tool is a more suitable for that purpose then extract from assemblies.
Could you please clarify:

1. Can I use it for single isolates rather than metagenomes?
2. Can it deal with potentially new genera (not sure how it will match with Silva db)?
3. If I will get several rRNA copies from single isolate, how I should deal with them?
   Thanks