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skovaka / UNCALLED

Raw nanopore signal mapper that enables real-time targeted sequencing
MIT License
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Computer Specifications #39

Open Kav57 opened 2 years ago

Kav57 commented 2 years ago

I am interested in using UNCALLED, can you give me an idea of the specification of computer required to run this to exclude the human genome in real time? Specifically, is a GPU required? Which Nanopore devices is it compatible with?

skovaka commented 2 years ago

UNCALLED does not require a GPU, and it's compatible with MinION and GridION. However, unfortunately we currently can't handle the full human genome, as we are limited to sequences less than ~1Gbp. I recommend you look into ReadFish (https://github.com/LooseLab/readfish), or the "adaptive sampling" option built into MinKNOW. A GPU is recommended for those methods, but you may be able to get away with a high-end CPU.