Question: Oxford Nanopore error rate?
1
gravatar for stacy734
3 months ago by
stacy73440
stacy73440 wrote:

I'm considering trying the Oxford Nanopore sequencer.

I know at one point they had a very high error rate, which they advertise as being much lower now. I'm looking for a recent paper from an unbiased source that has tested what the error rate is in a real world process.

I have emailed the company repeatedly but they have not provided any information other than a link to the order page.

Thanks for any advice.

error oxford nanopore rate • 749 views
ADD COMMENTlink modified 3 months ago by WouterDeCoster40k • written 3 months ago by stacy73440

Do you have a reference available for organism you are working with?

ADD REPLYlink written 3 months ago by genomax71k

No, sadly there is no reference genome available. This would be for de novo assembly.

ADD REPLYlink written 3 months ago by stacy73440

As part of HGSVC one sample was sequenced with Oxford Nanopore (~1.5 years ago). You can browse the QC information of that sample here, just select "DNA-Seq, Oxford Nanopore" from the set of reference data sets. The "Summary stats" tab lists the error rates of this data set for mismatches, insertions, and deletions computed using Alfred. The combined error rate was ~12%.

ADD REPLYlink written 3 months ago by trausch1.4k
3
gravatar for WouterDeCoster
3 months ago by
Belgium
WouterDeCoster40k wrote:

a recent paper from an unbiased source

Well, I'm not sure if I fit those requirements, but the quality score distribution of a sample of our human MinION and PromethION data, sequenced a year ago and base called a couple of months ago looks like this:

enter image description here

ADD COMMENTlink written 3 months ago by WouterDeCoster40k

Thank you WouterDeCoster for posting this image.

Can you post the title of the paper? I'd like to read it for more details.

ADD REPLYlink written 3 months ago by stacy73440

You can find our manuscript here: https://www.biorxiv.org/content/10.1101/434118v2

ADD REPLYlink written 3 months ago by WouterDeCoster40k
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