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Old 08-28-2009, 01:28 AM   #1
vani s kulkarni
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Default velvet and SOAPdenovo assembly

hi
I have used the velvet and SOAPdenovo for my solexa reads.
Can any one explain how can I compare cotig from both results?
I have used the same k-mer in both case.

And

I know that people use R for looking at the good contigs (by plotting with k-mer and other parameters), how to do that to judge K-mer or hashlength?

Thanks
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Old 08-28-2009, 07:47 AM   #2
bioinfosm
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For starters you may look at number of contigs, n50, how they map to a close by organism, or what do the contigs map to ...
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