Forum: Using Graphics Processing Units (GPUs) in bioinformatics
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gravatar for Denis
28 days ago by
Denis120
Denis120 wrote:

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?

algorithm gpu forum • 255 views
ADD COMMENTlink modified 28 days ago by ATpoint23k • written 28 days ago by Denis120
1

Hi,

I have removed the extraneous code commenting you had in your post. Please use these formatting options appropriately. Also, this topic seems more like a forum discussion than a question with well defined "correct" answers, so I will change it to a Forum discussion.

ADD REPLYlink written 28 days ago by RamRS24k
2
gravatar for jared.andrews07
28 days ago by
jared.andrews073.1k
St. Louis, MO
jared.andrews073.1k wrote:

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.

ADD COMMENTlink modified 28 days ago • written 28 days ago by jared.andrews073.1k
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gravatar for WouterDeCoster
28 days ago by
Belgium
WouterDeCoster41k wrote:

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.

ADD COMMENTlink written 28 days ago by WouterDeCoster41k
1

Yeah, this is a good point, machine learning packages will often attempt to make use of them, particularly during model training.

ADD REPLYlink written 28 days ago by jared.andrews073.1k

See also https://developer.nvidia.com/Clara-Genomics, and googling "GPU aligner" already returns plenty of hits.

ADD REPLYlink written 28 days ago by WouterDeCoster41k
1
gravatar for ATpoint
28 days ago by
ATpoint23k
Germany
ATpoint23k wrote:

HiCCUPS uses GPUs to identify chromosomal loops in HiC data https://github.com/aidenlab/juicer/wiki/HiCCUPS.

ADD COMMENTlink modified 28 days ago • written 28 days ago by ATpoint23k
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