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Old 05-15-2009, 01:08 PM   #1
bioinfosm
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Default 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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Old 05-17-2009, 10:24 PM   #2
francesco.vezzi
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Quote:
Originally Posted by bioinfosm View Post
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
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 together
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Old 05-18-2009, 12:41 AM   #3
jvhaarst
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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.
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Old 05-18-2009, 10:26 AM   #4
jts
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Have you considered using abyss?

http://www.ncbi.nlm.nih.gov/pubmed/19251739
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