SOAPdenovo -reference genome

[guru1985]

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.

[melop]

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.

Ray