Possibility of a de-novo assembly but with a gene as starting point/reference?
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7.9 years ago

I am trying to de-novo assemble a cyanobacterium genome and I'm wondering whether I could use a characterized gene as a kind of reference or "seed" sequence? Is this possible using SPAdes' reference-based assembly? There are multiple reports of the conservation of this specific gene cluster that I've been reading about and it's rather large at 3.2Kbp. In connection to this, the 16S rDNA of the cyanobacterium has also been characterized so could I use that to make a starting point for assemblies?

Assembly genome sequencing • 1.1k views
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I don't think it works the way you are thinking (if I am understanding the gist of your post). A seed would help with local assembly but it would not allow the assembly to grow/eventually span the entire genome.

See this for some options, if you have a related genome avaialble: what should I use for reference guided assembly of bacterial genomes intended for comparative genomic analyses?

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