I have isolated a virus (phage), sequenced it, and ran a taxonomic search using Kraken. The most similar taxa is phage BT-1011:

Then, I created a consensus sequence with BBmap and mapped against the genome of this virus. With fastANI, I got the visualization of the mapping:

There are two issues I am not sure about:

1. There is still a large portion of the genome that is not classified (the pink area in the first plot).
2. The genome of the isolate is much smaller than the reference (second plot).

I fear that the mapping against BT-1011 has left out a large chunk of genome.

My question is: what is the correct procedure for the assembly of a phage genome?

Would the mapping against the most closely related phage be enough (as I did)?

Or shall I generate a de novo assembly and leave it as is?

NOTE: I made such an assembly but I got several contigs; how can I get a single consensus sequence from those?

Thank you