Question: ONT fast5 basecalling
0
gravatar for a.lapin
12 months ago by
a.lapin0
a.lapin0 wrote:

Greetings!

I have a lot of ONT sequencing data in .fast5 format and I need to perform a basecalling via guppy_basecaller. The problem is that computation will take about 1.5-2 months, because I don't have a decent GPU and have to perform the basecalling using CPU. The question is can I just split the data (from one sequencing run) and perform the computation on multiple PC's?

ADD COMMENTlink modified 12 months ago by WouterDeCoster45k • written 12 months ago by a.lapin0
2
gravatar for WouterDeCoster
12 months ago by
Belgium
WouterDeCoster45k wrote:

Yes, that's perfectly fine. If you can get access to a large cluster or server then that would also make things faster.

ADD COMMENTlink written 12 months ago by WouterDeCoster45k

Thank you. Everything really worked well, the calculations took less than a week. But I have another question, where can I read something about quality scoring in ONT reads? I can not find any information about encoding.

ADD REPLYlink written 12 months ago by a.lapin0

It's the same Phred quality score as other sequencing data: https://en.wikipedia.org/wiki/Phred_quality_score

ADD REPLYlink written 12 months ago by WouterDeCoster45k

Hi @WouterDeCoster, do you have a guide for basecalling using Guppy ? (I don't have access to the community page)

ADD REPLYlink written 8 months ago by Picasa590

What's unclear after reading the command line help?

ADD REPLYlink written 8 months ago by WouterDeCoster45k
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