find connections between clusters (supercluster)

[ferrojm]

Hi,
I am looking to assemble contigs that may connect clusters within the same supercluster. I was unable to find this information/reads on RepeatExplorer so I started trying SeqGrapheR, is this possible?

For example, if I want to assemble the contigs that may connect two clusters (e.g., CL43 <---> CL28)

I was thinking of importing CL43, using the blastn tool to blast reads.fa from CL28 against CL43, and then assembling those reads.
Does SeqGrapheR has any tool to directly visualize connections? Do you think this is a good approach or could you suggest any pipeline or paper to assist me with this?

I would really appreciate any guidance on this matter!