Have you considered using abyss?
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I'm in the process of doing just that (1GB genome done with Illumina data), I'll post my results.
I'll first have a go with SOAPdenovo, see where that leads me.Leave a comment:
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The best de novo assembly tool is velvet but also euler-sr gives good performances. I think is quite hard assembly a so large amount of data, I think you are oblige to divide it into several sets and assembly independently and then try to combine the results togetherOriginally posted by bioinfosm View PostLeave a comment:
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a GB genome with SE PE data
1gb + genome, 100gb + sequence data (solexa)
What are people's thoughts for de novo assembly? RAM being the limiting issue, and of course the speed and accuracy if less of RAM is used
and there are a lot of deNovo assembly tools which I was unfortunately not able to follow .. so your feedback is very welcome.
thanks
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