Input parameters GS de novo Assembler

grassgirl · 06-03-2011, 12:40 PM

Hi forum members,

I am just getting my feet wet with sequence analysis, analyzing a small set of cDNA data from a 454 Junior run. I did a successful assembly on the GS de novo assembler and now I am wondering about input parameters such as seed step, seed length, etc. I understand what these are conceptually, but I am wondering how I would want to change them from the defaults and why. In other words, what is the ultimate goal with an assembly and how do these inputs affect it. Fewer contigs/isotigs? Or...?

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06-03-2011, 12:40 PM	#1
grassgirl Member Location: Oregon, USA Join Date: Mar 2011 Posts: 51	Input parameters GS de novo Assembler Hi forum members, I am just getting my feet wet with sequence analysis, analyzing a small set of cDNA data from a 454 Junior run. I did a successful assembly on the GS de novo assembler and now I am wondering about input parameters such as seed step, seed length, etc. I understand what these are conceptually, but I am wondering how I would want to change them from the defaults and why. In other words, what is the ultimate goal with an assembly and how do these inputs affect it. Fewer contigs/isotigs? Or...?