Reference Genome for Eukaryotes

[GabrielaPinho]

Dear Bao,

I want to extend the scaffolds of an Eukaryote assembly, I have the reads and the scaffolds of my focus species, and would like to know how the reference genome should be organized. Should I join all the reference chromosomes to input it in AlignGraph?

Thank you,
Gabi

[baoe]

Hi, Gabi,

Sorry for reply late. I don't think you need to join all the reference chromosomes. You can put them in the same file and run AlignGraph. AlignGraph processes them one by one.

Bao