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Old 11-22-2014, 04:56 PM   #9
Brian Bushnell
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Location: Walnut Creek, CA

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Quote:
Originally Posted by GenoMax View Post
With PacBio you would have a good chance of finishing the genome (with productive libraries, of course). I have no experience with optical mapping and can't say if that option would offer similar odds.
I agree. Similarly, I have no experience with optical mapping, but I do know that when we sequence a bacteria with 2 SMRT-cells, we usually end up with a single contig, unless of course the organism has additional plasmids.

Since you already have such a nearly-complete genome it's unfortunate to have to completely resequence it. But, I will say one thing...

2.5 Mbp is extremely small. With a single SMRT-cell, using the latest chemistry, if you have good yield (at least 80x coverage, or ~200Mbp) you will probably get a 1-contig assembly. Down to 60x... maybe 1 contig, more likely 2.
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