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Old 08-11-2017, 07:14 AM   #6
cstack
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Location: Florida, US

Join Date: May 2017
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Quote:
Originally Posted by colindaven View Post
Good idea. If I were you I'd go for as much Nanopore as I could afford, eg 30X, then create an assembly from this alone using Canu..
We work on a plant species that is difficult to get DNA from, and from our first few flowcells we were getting approx. 3-5Gbp of 1d reads (using 9.4 chem w/ the standard ligation kit). If you get something similar then it would only take 2-3 flow cells to (in theory) reach 30X coverage.

Also, I think the typical canu pipeline has an overlap error correction step. I've never looked at the coverage needed for this to be really effective, but I bet 30X would be at the lower end. I agree with colindaven about hybrid assembly -- it can get really messy. If you can build some nice scaffolds with ONT data, then you might be able to simply map the illumina reads and call a consensus from this. I'd be very interested to hear how you or others would approach this!
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