how to deal with the ccm results

[lilinzhou]

I am currently trying to split the raw reads by chromosome, and I have a few draft assemblies based on Canu, Nextdenovo, Flye, and Necat. However, the scaffold numbers ended up differently based on draft assemblies after the ccm module, and I also didn't know the real chromosome number of this species (no reference). It would be helpful if you could tell me which scaffolding results (or how to choose) should I use, since they will be of great importance to the assembly step after the raw reads have been split based on scaffolding.

[avdanurag]

Hi Mohamed,

Even I am facing the same issue. I get different scaffold numbers based on draft assemblies after the ccm module. My species have 12 chromosomes. A few drafts show 6 scaffolds, while others show 13 scaffolds. Can you please suggest How should I proceed further?

[ccduty]

Same confusion