Question: MinION nanopore sequencing quality
0
gravatar for 984366176
2.8 years ago by
98436617620
98436617620 wrote:

the MinION quality scores do not follow Phred expected error rates, according to a paper that is Assessing the performance of the Oxford Nanopore Technologies MinION .Each base has a quality score, I want to know how to compute the MinION quality scores .

sequencing • 4.5k views
ADD COMMENTlink modified 2.8 years ago by igor8.6k • written 2.8 years ago by 98436617620
1

Your question is unclear, please provide more information.

ADD REPLYlink written 2.8 years ago by WouterDeCoster41k

I have updated this question,thanks for any suggestion.

ADD REPLYlink written 2.8 years ago by 98436617620

Quality scores corresponding to nucleotides are calculated by the software used for basecalling. Dependent on when the data was generated this is either a Hidden Markov Model (HMM) or a Recurrent Neural Network (RNN). You can't compute those basecall quality scores yourself, and I also don't understand why you would want to.

Since you are still vague in your question concerning which paper this is from I cannot help you further with that.

ADD REPLYlink written 2.8 years ago by WouterDeCoster41k

My question might not be clearly stated. I know I can't compute those basecall quality scores.I just want to know the detailed algorithm for quality scores.Thanks

ADD REPLYlink written 2.8 years ago by 98436617620

Then try to be complete from the beginning when you ask your question.

I don't think the exact algorithms are disclosed by ONT.

ADD REPLYlink written 2.8 years ago by WouterDeCoster41k

That's why I can't find the related information.Thank you very much.

ADD REPLYlink modified 2.8 years ago • written 2.8 years ago by 98436617620

So are those quality scores different than what Illumina ould have? like the Q-score?

ADD REPLYlink written 23 months ago by KVC_bioinfo410

The idea is the same: likelihood of having that nucleotide at that position. But as the chemistry and signal is fundamentally different the calculation of phred scores will be different as well. But they mean the same.

ADD REPLYlink written 23 months ago by WouterDeCoster41k

In case you were not aware, ONT has their own support forum. It might be helpful to ask there as well: https://community.nanoporetech.com/posts

ADD REPLYlink modified 2.8 years ago • written 2.8 years ago by igor8.6k

According to his answer C: the content of FAST5 files that are generated from MinION he won't have access to that forum.

ADD REPLYlink written 2.8 years ago by WouterDeCoster41k

Good point. I didn't see the other thread (where you had essentially the same suggestion).

I assumed he was working with his own reads.

ADD REPLYlink written 2.8 years ago by igor8.6k
3
gravatar for igor
2.8 years ago by
igor8.6k
United States
igor8.6k wrote:

You can use an open source basecaller (such as Nanocall) if you want to know the exact algorithm. The results are supposed to be comparable to the official ONT basecaller.

Nanocall has a fair amount of background info on their website: https://github.com/mateidavid/nanocall

ADD COMMENTlink written 2.8 years ago by igor8.6k
1

This is interesting to see, thanks.

However, it seems that since the release of Nanocall, ONT have open-sourced Metrichor, and the quality of nanocall doesn't hold up on the latest chemistry.

From the nanocall github:

If you want to use Nanocall on R9 data, Nanocall does support it directly, but its accuracy is significantly lower than that of Metrichor (unlike the case of R7.3, where the two had similar accuracy). The reason for the discrepancy is that Metrichor on R9 uses a more elaborate RNN-based approach, compared to the simple HMM-based one in Nanocall.

ADD REPLYlink written 2.8 years ago by Daniel3.7k
1

The Metrichor source code was opened (under a development license).

ADD REPLYlink written 2.8 years ago by 98436617620

Which is pretty damn restrictive...

ADD REPLYlink written 2.8 years ago by WouterDeCoster41k

Oh. I didn't see that. Good to know.

ADD REPLYlink written 2.8 years ago by igor8.6k
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