kallisto on gpu

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Miriam Zuckerbrot

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May 24, 2023, 10:41:43 AM5/24/23
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Is there a way to make kallisto GPU accelerated?

Thanks

Pall Melsted

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May 24, 2023, 1:36:14 PM5/24/23
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No, and it is not worth it. Most of the time comes from lookups in a hashtable which is very hard to accelerate on GPUs. 

- Pall

On Wed, May 24, 2023 at 2:41 PM Miriam Zuckerbrot <mzuck...@gmail.com> wrote:
Is there a way to make kallisto GPU accelerated?

Thanks

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Lior Pachter

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May 24, 2023, 1:46:45 PM5/24/23
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I agree with Páll, but will just add that NVIDIA has worked on this; see https://docs.nvidia.com/clara/parabricks/3.8.0/documentation/tooldocs/man_kallisto.html
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