Reproducibility of CLC de novo assembler

corthay · 04-16-2010, 01:35 AM

Hi,

I've used CLC de novo assembly to assemble 454 data but
I coundn't get reproducible result as the results are always
a bit different. I would like to know the reason why the
assembler generate different result each time even if I use
same parameters.
The version of clc_novo_assemble is 3.03.45409

I would appreciate any form of help
Thanks,

Corthay

sujaikumar · 06-03-2010, 06:07 AM

Hi Corthay

Quote:

Originally Posted by corthay

Hi,
I've used CLC de novo assembly to assemble 454 data but
I coundn't get reproducible result as the results are always
a bit different. I would like to know the reason why the
assembler generate different result each time even if I use
same parameters.

My understanding is that it uses SIMD (hence is scarily fast) and the way it splits up data each time (to run in parallel on all cores of your machine) is random, hence the slight differences.

One way to test this would be to restrict the process to one core (by running it on a virtual machine? Or does anyone know if there a cool linuxy/unixy way to do this?)

Cheers,

- Sujai

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04-16-2010, 01:35 AM	#1
corthay Member Location: japan Join Date: Oct 2008 Posts: 25	Reproducibility of CLC de novo assembler Hi, I've used CLC de novo assembly to assemble 454 data but I coundn't get reproducible result as the results are always a bit different. I would like to know the reason why the assembler generate different result each time even if I use same parameters. The version of clc_novo_assemble is 3.03.45409 I would appreciate any form of help Thanks, Corthay Last edited by corthay; 04-16-2010 at 01:42 AM.