Abyss merge multiple assemblies

[carojasq]

Hi all.

I've made several de novo genome assemblies using Abyss, for my libraries i have used 25,30,35,40,45,50,55,60,65 as kmer value. The best assembly that I've got is using 55 as kmer value.

I have tried to merge the assemblies using minimus2 pipeline, but it took several days making overlapping step (20 days) and never ends!, I've seen that this pipeline runs in one core and don't have option for use multiple cores. I followed this tutorial: http://ged.msu.edu/angus/metag-assem...et-multik.html

The question is: There is another strategy or tool to integrate these assemblies?

[flobpf]

Which assemblies are you trying to merge? I'm confused because you say your best assembly is with 55 kmer. Why not just stick with that? That's what typically done.

FYI, on the page above it says

We’re currently using the minimus2 approach, because we think it does a decent job, but we can’t really justify it to you yet .

Minimus and Velvet work best with small genomes. For large genomes, I've had Minimus run fine with merging two assemblies.