Question: Guppy basecaller ONT
0
gravatar for zoegward
9 days ago by
zoegward60
zoegward60 wrote:

Hi, I'm a complete beginner at ONT. I've read that you can use Guppy for basecalling for the Oxford Nanopore Technology. Could someone point me to a tutorial/reference manual/ test data??? I can't seem to find much information on this anywhere???

ont • 250 views
ADD COMMENTlink modified 8 days ago • written 9 days ago by zoegward60
2

@Wouter de Coster (biostars ONT expert) should have something more detailed for you tomorrow but in the mean time take a look this post to find the links to download the basecaller from. I hope you have a compatible GPU to run it on.

ADD REPLYlink written 9 days ago by genomax65k
1

Guppy also works on CPUs, although indeed much faster on a GPU. But that may not matter that much if you're not processing tons of data.

ADD REPLYlink written 9 days ago by WouterDeCoster38k

Is he putting out a tutorial on basecalling?

You can check this out for details on guppy parameters.

ADD REPLYlink modified 9 days ago • written 9 days ago by BioinformaticsLad80
2

Is he putting out a tutorial on basecalling?

According to my sources, no :-D

ADD REPLYlink written 9 days ago by WouterDeCoster38k

Wouter de Coster (biostars ONT expert) should have something more detailed for you tomorrow

What did genomax mean by this? I thought he might be referring to a tutorial or paper.

ADD REPLYlink modified 9 days ago • written 9 days ago by BioinformaticsLad80
1

Genomax was essentially creating high expectations. But I don't think any tutorial or paper I could write would improve on the official documentation, so I won't.

ADD REPLYlink written 9 days ago by WouterDeCoster38k

@BioinformaticsLad: Problem is that the community you posted a link to is not open. It requires an invite/purchase from ONT to join.

ADD REPLYlink modified 8 days ago • written 8 days ago by genomax65k

Yes, I have raised this issue in the ONT community. I would have to look into terms and conditions to check what I can share outside of the community.

ADD REPLYlink written 8 days ago by WouterDeCoster38k

I could access the link - thank you. Could you clarify something for me? I was just told that you can either get base calls directly from the grid/minion (via Guppy) or use the fast5 files to base call with Guppy separately. Is this correct? If so, is there an advantage/disadvantage to base calling separately??

ADD REPLYlink written 8 days ago by zoegward60
3

That's right. You can basecall the fast5 files separately (from sequencing).

Advantages of separating the processes: 1) You're sequencing on a minION and have a weak PC. Simultaneously basecalling can slow things down. You can move your fast5 files to a much faster PC for more efficient basecalling. 2) You want to basecall using something other than Guppy. 3) You want to re-basecall your old fast5 files using an updated & improved basecaller (ONT updates their software regularly giving incremental increases in accuracy).

Disadvantages: 1) No real-time data stream of reads and/or real-time analysis (eg. EPI2ME) 2) If you have a GridION, basecalling is fast enough to keep up with sequencing so separating the processes will take you longer to get to reads. 3) You can't see the quality of your reads during the run.If you could, you might decide to stop the run due to low quality reads. 4) I've heard that (on Promethion at least) using all flowcells simultaneously sequencing and basecalling can slow things down.

ADD REPLYlink modified 8 days ago • written 8 days ago by BioinformaticsLad80
1

Thanks for that - most informative and very much appreciated.

ADD REPLYlink written 8 days ago by zoegward60
0
gravatar for Vijay Lakhujani
9 days ago by
Vijay Lakhujani4.0k
India
Vijay Lakhujani4.0k wrote:

I agree to genomax 200 % ; WouterDeCoster is the best person to answer!

However, if you have access to nanopore community page then this link is the best place to look at

ADD COMMENTlink written 9 days ago by Vijay Lakhujani4.0k
1

That link would definitely answer most, if not all questions. Can you access it zoegward ? Let us know if there is anything more specific you struggle with.

ADD REPLYlink modified 9 days ago • written 9 days ago by WouterDeCoster38k

WouterDeCoster, that link is dead

ADD REPLYlink written 9 days ago by Vijay Lakhujani4.0k

I was talking about your link. My link was just tagging OP, but it seems the trailing ? corrupted it :) (changed it now)

ADD REPLYlink written 9 days ago by WouterDeCoster38k

strange, i still see this

Screenshot-from-2019-04-16-14-59-29

ADD REPLYlink modified 9 days ago • written 9 days ago by Vijay Lakhujani4.0k

Oh yes, there is some weird issue with OPs user profile. I forgot. I already informed Istvan Albert

ADD REPLYlink written 9 days ago by WouterDeCoster38k
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