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Oxford Nanopore MinION – USB stick-sized DNA sequencer

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Re: Oxford Nanopore MinION – USB stick-sized DNA sequencer

#31
post #8

The error rate in the "good part" is about 15%. That is quite frankly very very very poor. This might be a good alternative to pacbio, (unless the other technologies can increase their read lengths). Typically (I chatted with my contacts at the Venter Institute)... best results are gotten by making long reads using pacbio or (maybe minion, they are looking into that currently) and using that to generate the scaffold…

All depends on the application and the price per base. If it's cheap enough, you can average over more reads, even with higher error rates. The error rate should come down though. I guess the price will also come down a lot.

I think the single molecule approach has both advantages and disadvantages. Also I think that Illumina's technology in some sense also only reads parts of single molecules, and the averaging is done later in-silico, much as the nanopore would do also.

Re: Oxford Nanopore MinION – USB stick-sized DNA sequencer

#32
post #5

Earlier quoted context omitted.

No, it does not. You still need a wetlab to do sample preparation. There are a couple reasons why this is exciting though. Oxford Nanopore has seemed like bogus vaporware for several years now, and many people were skeptical that they had a viable product. This data release is the strongest suggestion yet that the thing actually works (but is still in no way conclusive). Two, assuming it does work, being able to sequ…

How portable is a "wetlab"? Could I take this with me into the jungles of south america or the se asia?

It might be possible to do the preparation steps with portable gear. "Classic" DNA extraction with multiple rounds of electrophoresis or PCR aren't strictly necessary for all applications.

Still, it would be easier to carry the sample back with you rather than carry the equipment into the djungle.

On the other hand a lab in a developing country might have less trouble using the MinION rather than sending away the samples for sequencing.

Re: Oxford Nanopore MinION – USB stick-sized DNA sequencer

#33
post #5

Earlier quoted context omitted.

No, it does not. You still need a wetlab to do sample preparation. There are a couple reasons why this is exciting though. Oxford Nanopore has seemed like bogus vaporware for several years now, and many people were skeptical that they had a viable product. This data release is the strongest suggestion yet that the thing actually works (but is still in no way conclusive). Two, assuming it does work, being able to sequ…

How portable is a "wetlab"? Could I take this with me into the jungles of south america or the se asia?

It might be possible to do the preparation steps with portable gear. "Classic" DNA extraction with multiple rounds of electrophoresis or PCR aren't strictly necessary for all applications.

Still, it would be easier to carry the sample back with you rather than carry the equipment into the djungle.

On the other hand a lab in a developing country might have less trouble using the MinION rather than sending away the samples for sequencing.

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