SEQanswers

SEQanswers (http://seqanswers.com/forums/index.php)
-   Bioinformatics (http://seqanswers.com/forums/forumdisplay.php?f=18)
-   -   Reproducibility of CLC de novo assembler (http://seqanswers.com/forums/showthread.php?t=4747)

corthay 04-16-2010 01:35 AM

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

sujaikumar 06-03-2010 06:07 AM

Hi Corthay

Quote:

Originally Posted by corthay (Post 17091)
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


All times are GMT -8. The time now is 08:18 AM.

Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2021, vBulletin Solutions, Inc.