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Old 03-27-2009, 09:00 AM   #6
doxologist
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Location: USA

Join Date: Jan 2009
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Quote:
Originally Posted by mchaisso View Post
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
thanks - looking forward to the update.
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