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Greetings,
I'm trying to use Velvet1.0 to map and assembly Illumina reads to a reference Newbler 454 assembly (fasta scaffolds with gaps as N's). Done this before with contigs not containing N's and it works beautifully but this time, it seems I'm getting an assembly that ends up with the contigs and doesn't retain the scaffolds in the final assembly (ie. the N50 and Nmax are much smaller). I can see how this could happen, the N's breaking the scaffolds. Anyone have any thoughts on how to get around this and/or another way of going about it (ie.) mapping and doing reference guided assembly without losing the scaffolds?
I'm trying to use Velvet1.0 to map and assembly Illumina reads to a reference Newbler 454 assembly (fasta scaffolds with gaps as N's). Done this before with contigs not containing N's and it works beautifully but this time, it seems I'm getting an assembly that ends up with the contigs and doesn't retain the scaffolds in the final assembly (ie. the N50 and Nmax are much smaller). I can see how this could happen, the N's breaking the scaffolds. Anyone have any thoughts on how to get around this and/or another way of going about it (ie.) mapping and doing reference guided assembly without losing the scaffolds?