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KolmogorovLab / hapdup

Pipeline to convert a haploid assembly into diploid
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GPU support #4

Closed MichelMoser closed 2 years ago

MichelMoser commented 2 years ago

Hi,

I guess, currently there is no GPU allowance for the PEPPER step in the hapdup pipeline?

Is the speed benefit too small to implement it for human sized genomes?

Cheers, Michel

MichelMoser commented 2 years ago

i see you disabled CUDA to redue image space. fair move =)

mikolmogorov commented 2 years ago

Yes, PEPPER supports GPU, but all other tools don't. So the speed gain is overall little, and currently does not worth added complexity.