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Old 02-11-2010, 06:54 AM   #1
Location: it

Join Date: Oct 2009
Posts: 40
Default velvet denovo

Hi ..I was running velvetg with various parameters but for different coverege cutoff iam getting the different to optimize the coverege cutoff ..

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Old 02-11-2010, 07:07 AM   #2
Location: Udine (Italy)

Join Date: Jan 2009
Posts: 50

In the manual there is a description of how generate an histogram that can help you in decide several parameters.
In general the best way to proceed is make some test on a little data set. You keep the parameters that give the best result on the small data set and you use them on the whole data set

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Old 02-11-2010, 07:35 AM   #3
(Jeremy Leipzig)
Location: Philadelphia, PA

Join Date: May 2009
Posts: 116

you should also look at N50, read usage, and the count of 1k contigs

the script in my sig might help you
Jeremy Leipzig
Bioinformatics Programmer
My blog
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