Question

ONT fast5 basecalling

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4.8 years ago

a.lapin • 0

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?

oxford nanopore fast5 sequencing basecalling • 3.3k views

ADD COMMENT • link updated 4.8 years ago by WouterDeCoster 47k • written 4.8 years ago by a.lapin • 0

score 2 · Answer 1 · 2020-02-27

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4.8 years ago

WouterDeCoster 47k

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

ADD COMMENT • link 4.8 years ago by WouterDeCoster 47k

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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 REPLY • link 4.8 years ago by a.lapin • 0

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

ADD REPLY • link 4.8 years ago by WouterDeCoster 47k

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