Falcon-Phase second round for scaffolding

Question

[Juke34]

After having phased my genome with HiC data using Falcon-phase, I would like to apply what they call the "second round" to perform the scaffolding.

The only concrete piece of information I found is here: https://github.com/phasegenomics/FALCON-Phase/issues/58

I'm stuck at step 6. It's probably something obvious as I don't find the information anywhere, but I'm quite unsure what tool/command I'm suppose to run.

I'm looking for some guidance.

Answer 1

[Juke34]

They answered me on github. I will probably write a more detailed protocol.