very fragmented draft genome
sqwwww opened this issue · 0 comments
sqwwww commented
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?