ABySS

Question

ABySS

sklages opened this issue 9 years ago · 2 comments

Hi,

any experience in using the output data with abyss? E.g. what best to take as MP and/or PE data for assembly?

Answer 1 · 2015-09-17T09:17:32.000Z

I don't have any experience with ABySS. From my (limited) understanding, ABySS can assemble paired ends and then scaffold with a long insert library.

Do you have a separate PE library in addition to your Nextera MP library? In that case, I think you would assemble using the PE library and then scaffold using the MP library. Using the --justmp flag will generate as many mate-pairs as possible which could then be fed to the ABySS scaffolder.

Answer 2 · 2015-09-17T09:30:20.000Z

thanks for the fast response. That's what I thought too. I do have separate PE libs (2).