Re: [wgs-assembler-users] 454 paired-end + wgs assembly

[Walenz, B. <bw...@jc...>]

Hi, Santino-

Without knowing what you’re assembling, I’d say you should put nothing in the spec file.  The biggest knob to change is utgErrorRate (default 0.03).  Lower can separate repeats, or fail to assemble anything.  Higher can overcome polymorphism, or over collapse repeats and duplications.  The second biggest knob would be unitigger=bog vs unitigger=bogart.  Bogart is still ‘experimental’ in the 7.0 release; better in CVS tip.

You might get better compute performance by setting the various “concurrency” options (especially cnsConcurrency) to the number of CPUs you have, and tuning overlapper for your hardware.  Generally, the defaults work well for something this size.

b
--
Brian Walenz
Senior Software Engineer
J. Craig Venter Institute


On 4/5/12 1:14 PM, "Santiago Revale" <san...@gm...> wrote:

Hello everybody!

I'm new to paired-ends assembly, so I'm hoping you could help me.
I have two 454 FLX Titanium libraries: one single-end (common wgs) and one pair-end (8Kb).

I ran sffToCA two times, one for each library, using "-trim chop" for the pair-end library (amongst other paired-end parameters).

Now, what parameters you suggest should I put in the specFile to perform this assembly for better results?

Thank you very much in advance.

Best,

Santino