aidenlab/3d-dna

very fragmented draft genome

sqwwww opened this issue · 0 comments

Hi,
I'm trying to scaffolding a draft for which the contigN50 is 8k. It's a very fragmented draft with more than 800 million contigs in it. I ran 3d-dna with default parameters, and put the output image in the attachment. Nearly half of the draft didn't assembled.

I have checked the parameters mentioned in DNA zoo, and I know I should adjust the -i smaller, I will try to run 3d-dna with -i 5000.

Is there any other parameters I should also pay attention to for the very fragmented draft? could you give me some suggestions?
a9b47cb8b587cb260b3bda63123089b