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Old 09-07-2011, 02:01 PM   #1
mihir.karnik
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Default Meta-Velvet

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?
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Old 12-21-2011, 09:24 AM   #2
gridbird
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ABYSS assembler can be used for huge data assembly.
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Old 03-26-2012, 03:10 AM   #3
colindaven
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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 ?
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Old 03-26-2012, 10:09 AM   #4
gridbird
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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?
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Old 03-27-2012, 03:41 AM   #5
colindaven
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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.
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