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Old 09-14-2010, 05:00 PM   #1
sulicon
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Default Different results generated by using the same parameters

I'm new to 2nd-generation sequencing data analysis. I have found that every time I run newbler, the de novo assemlber from Roche, I get different results... The parameters used are identical in these runs. Is this normal?

update:
It seems that the difference is caused by multiple CPUs used for computation. I had used "-cpu 10" before. If only one CPU used, the result is reproducible, although it's also different from results generated by multiple CPUs...

Last edited by sulicon; 09-14-2010 at 05:23 PM. Reason: update
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Old 09-20-2010, 06:57 AM   #2
flxlex
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What you find is correct, only with -cpu 1 will you get the same results each time. Nice to be able to answer one's own question, eh?
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Old 09-20-2010, 11:59 PM   #3
Torst
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Quote:
Originally Posted by sulicon View Post
I'm new to 2nd-generation sequencing data analysis. I have found that every time I run newbler, the de novo assemlber from Roche, I get different results... The parameters used are identical in these runs. Is this normal?
There seems to be two ways to get different results from gsAssembler:

1. As you found, the -cpu option with more than 1 cpu gives different results! The only reliable way is with -cpu 1.

2. The order you supply your .SFF files on the command line changes the results, even with -cpu 1 enabled. It seems you need to put your paired reads AFTER your single-end reads.

I am appalled that just important software can be so non-deterministic in its operation!
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