Canu : how to increase the required coverage for the trimming and assembly?

Question

[celine.petitjean]

Hello,

I am using Canu 1.4 on a unix machine. I am trying to assemble a eukaryote genome with a lot of repeats. We have PacBio datas, and a coverage ~35x. We are obtaining quite good results, but it seems that we have problems of misjuction among out final contigs. I wanted to know if there is a possibility to require a higher coverage during the trimming and assembly phases.

thank you in advance. Celine

Answer 1

[colindaven]

Hi Celine,

it seems you're using a slightly older version of canu.

I would upgrade to 1.6 if I were you. https://github.com/marbl/canu/releases

Also, I would look through the issues on the canu github site to get an answer to your question. I'm positive many have had similar issues and had the same problems. Giving Canu different parameters can be tricky though in my experience.

Good luck