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Old 05-11-2012, 08:30 PM   #1
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Location: sydney

Join Date: Mar 2012
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Default SOAPdenovo -reference genome

Hi there

I am using SOAPdenovo for assembling a large genome (illumina reads). I have some contigs generated from transcriptome analysis of a similar organism and i wanna use it as a scaffold (reference) for assembling the genome of the target organism. Is it possible ? if so How ?

Any help would be greatly appreciated.
guru1985 is offline   Reply With Quote
Old 06-01-2012, 10:51 AM   #2
Location: college station

Join Date: Jan 2012
Posts: 22

Hi There,

I want to do the same thing too. We have some PE and SE illumina reads (30x total), a pretty fragmented genome from a closely related species and a 454 as well as a PE RNA-seq library. Now the question is how to get a good genome assembly out of it.
I'm thinking about RNAPath in the erange package. Don't have time to try it yet but it sounds like an interesting idea.

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