Meta-Velvet

[mihir.karnik]

Hi,

I have been using Meta-Velvet for assembling my nucleotide sequences. However, i have run into some issues as the size of my data is very large. Can anyone tell me if i can break my file up and then assemble it and still get the same results?

[gridbird]

ABYSS assembler can be used for huge data assembly.

[colindaven]

Can you
a) cluster data first ? Try CD-hit ?
b) remove contaminants first ?
c) get time on a large mem server ?
d) look into the cloud ?

[gridbird]

Hi Colindaven, it is a good idea. We really did several tests using CD-HIT before. We got better assembly results than original dataset. did you also use CD-HIT for assembly test?

[colindaven]

That's interesting. Nope, haven't used CD-Hit for metagenomic data before, but may have to do so soon depending on how much of our forthcoming metagenomics data is mappable.