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nanoporetech / megalodon

Megalodon is a research command line tool to extract high accuracy modified base and sequence variant calls from raw nanopore reads by anchoring the information rich basecalling neural network output to a reference genome/transriptome.
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Could I run megalodon without GPU? #284

Closed liangyong1991 closed 2 years ago

liangyong1991 commented 2 years ago

I want to know if megalodon could run successfully without GPU? If yes, how to set it? I have just use --devices cuda:N, it doesn't work!

marcus1487 commented 2 years ago

The default without specifying the --devices argument it to use CPU. Basecalling with CPU only resources is very very slow though. Expect speeds to be 100-1000 times slower for the high accuracy models.

liangyong1991 commented 2 years ago

Ok, thank you.