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  • 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.

  • #2
    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

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