After running circlator reduction of 6 genomes in assembly to 3.

[severst]

Hi,
I am using Rolling Circle Amplification technique which produces very long amplicons. After amplification, I fragment these products to approximately 1 genomelength and sequence this by MinION. I assembled the data with Canu, which ends up in an assembly of 6 times the genome length, since there were multiple reads >2 times the total length.
By using Circlator, I was able to reduce the assembly length to 3 times the genome.
Is it possible to reduce this to 1? Or do I have to manually cut my reads to succeed?
Thanks, Tim