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Old 03-27-2009, 08:59 AM   #5
doxologist
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Location: USA

Join Date: Jan 2009
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Quote:
Originally Posted by swbarnes2 View Post
Sharcgs, ssake, and vcake are...not the most sophisticated programs.

You want the kinds that use de brujin graphs. Velvet is genrally the most commonly used one, and it's constantly being updated and supported...I don't know that the others are you mentioned are.

There's also Euler-SR, and I think EDENA also works okay.

I haven't tried Euler yet, but I tried EDENA once, and it was way slower than velvet.

With low coverage solexa data, there's not going to be much you can do.
Velvet is only colorspace right?
I'm using parts of NextGENe which incorporates some de brujin graphs...
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