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Old 03-12-2013, 10:23 AM   #1
Location: USA

Join Date: Sep 2012
Posts: 41
Question De novo assembly (scaffolding)

I am performing de novo assembly on a non-model organism. I am using the clc denovo assembly tool. In the assembly options, there is an option of performing de novo including and excluding scaffolding. I would like to know what scaffolding means? I am still a newbie at this, and I have been searching for the definition of scaffolding but I keep getting various definitions. Could someone please help me out with this, or direct me to a post that has discussed scaffolding?

Another question I have is, what constitutes a good de novo assembly, especially of an organism with a genome size of ~500Mb? I have read some papers that say fewer count of contigs, large N50... what else should I look for? In short, could someone please give me a few tips on what steps I should take to have a good assembly and also maybe a few tips on what to look for so as to choose an optimal assembly (even if its directing to me a specific scientific paper, I will be extremely grateful!).
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