Question: Oxford Nanopore error rate?
1
gravatar for stacy734
26 days 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 • 172 views
ADD COMMENTlink modified 26 days ago by WouterDeCoster39k • written 26 days ago by stacy73440

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

ADD REPLYlink written 26 days ago by genomax68k

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

ADD REPLYlink written 26 days 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 26 days ago by trausch1.3k
3
gravatar for WouterDeCoster
26 days ago by
Belgium
WouterDeCoster39k 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 26 days ago by WouterDeCoster39k

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 26 days ago by stacy73440

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

ADD REPLYlink written 26 days ago by WouterDeCoster39k
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