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Old 02-27-2012, 06:47 PM   #41
BBoy
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Location: Pacific Northwest

Join Date: Oct 2010
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Quote:
Originally Posted by JamesH View Post
I've been thinking more about the disruption that the nanopore tech could cause, there's been a bit of discussion regarding the "niche" of de novo genome assembly, and granted this will be the first thing that people want to get their hands on a system to do (because of the long reads). But for me, "run until", and no library prep are what will probably make the bigger difference, you don't have to just do long reads: there's no reason not to put shorter fragments in. In our lab we do a lot of population genetics involving non-model plants and animals, this mostly involves genotyping a lot of individuals (usually at a cost of $10-30 per individual). While the cost of sequencing has been coming down the time/cost/hassle of library prep has been the main barrier for us in going NGS (having to maintain 100's of barcoded primers etc). Straight away I can see several ways that I can make restricted libraries for each individual, not bother with PCR and any associated errors, then run a Gb or two until sufficient coverage is reached and do genotyping by sequencing for close to the cost of what we currently do. The ability to do RNAseq gene expression studies in the lab without having to send off to a core facility (even if you have to make cDNA) will also be pretty awesome.
Yes, this is something that in my sniping about parallelism I seriously overlooked. There is nothing that prevents you from heavily fragmenting DNA and running short reads. In fact, there is nothing preventing you from running PCR and then sequencing if you have a specific need for a specific short segment. Shows you how easily I develop myopia...

Quote:
Originally Posted by JamesH View Post
I can also see applications for the USB stick in agriculture to allow field-based monitoring of resistance to insecticides/herbicides. I think that putting this kind of sequencing power straight into the hands of researchers is going to be a big game changer, and the more I think about it the less I can see myself doing a lot of the things that I currently do in the lab!
Absolutely, as long as the bio-informatics eventually are brought up to iPhone level, i.e., a big green and a big red button with little thinking in between.
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