Ah, gpus are cheating... :) What I meant about i/o is that if you're reading the data off of disc your read/write time is probably longer than 8 minutes. With S

Ah, gpus are cheating... :) What I meant about i/o is that if you're reading the data off of disc your read/write time is probably longer than 8 minutes. With SSDs you can obviously go faster. One problem with scaling is that you need a bunch of machines that have the gpus available (although if you can get the whole pipeline under 30min you wouldn't need many machines). The cloud genomics companies mostly use AWS and Google cloud for their compute and I don't know what sorts of non CPU compute resources are available. You would probably be interested in looking into Edico Genomics' Dragen FPGA. Is there a way to PM on HN?