Hi
I'd be interested in anyone who can tell me about software that will/can combine de novo assembled contigs with a reference assembly.
What I have are bacterial genomes and between 36 and 72bp reads.
When I align to the reference, large parts of the genome align perfectly, but then I find gaps; If I do a de novo assembly, I can see that some of the contigs span the gaps, but I am doing this by eye using MUMmer, IGV and a few other bits and bobs.
It seems to me obvious that someone would have written this, but I can't find anything....
Mick
I'd be interested in anyone who can tell me about software that will/can combine de novo assembled contigs with a reference assembly.
What I have are bacterial genomes and between 36 and 72bp reads.
When I align to the reference, large parts of the genome align perfectly, but then I find gaps; If I do a de novo assembly, I can see that some of the contigs span the gaps, but I am doing this by eye using MUMmer, IGV and a few other bits and bobs.
It seems to me obvious that someone would have written this, but I can't find anything....
Mick
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