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Old 03-26-2009, 06:03 PM   #4
mchaisso
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Location: Seattle, WA

Join Date: Apr 2008
Posts: 84
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The new euler-sr is starting to reach the ballpark, or finally the runtime order, of velvet for time, and hopefully in the next couple of days I'll tweak a couple of things that will speed it up still.

There is a tool in euler called assemblesec.pl, for assembly sans error correction, which just builds a de Bruijn graph, and hands you the result. You can parse the output to find which reads are on the same contig, or run some "light" error correction on the resulting graph.

However, you may want to use the error correction, since that can patch overlaps in low-coverage projects. It just takes forever. Currently euler-sr guesses the average coverage, but this goes bad in very high and very low coverage projects. In the release I'll post later tonight, there is an option to specify the minimal coverage (most likely 2).

-mark

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.
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