In our days GPUs have installed on many HPC clusters. I'm using HPC cluster for de novo assembly, SNP calling, reads mapping and other bioinformatic routines. I'm wondering for which bioinformatic tasks/algorithms i may apply GPUs? How can i benefit from using GPUs in my computations?
Mostly GPUs are allocated to jobs that have molecular modeling involved, as they allows thousands of calculations to be performed in parallel, which these tasks require. People trying to work with protein structures (or structures of other molecules like DNA/RNA) and particle dynamics are likely the ones at your institution who make use of them.
For what you're doing, they aren't going to be any more helpful than just running samples in parallel. Particularly since GPUs are quite expensive (relative to typical processors) and your cluster likely only has so many of them to go around.
GPUs are also used in basecalling of nanopore sequencing data, which use RNN machine learning approaches. Although I haven't looked into that further, I read things about people rewriting tools like aligners to make use of GPUs, but it's still very much a niche area.
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