I’m going to weigh in here if I may. Sorry, I don’t frequent these boards much (at all), but I have a lot of experience with Oxford Nanopore sequencing and GPU compute. First a collection of resources that may be useful to you:
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I have a document on selecting an appropriate GPU and compute set up for Nanopore data generation and analysis, I try to update this regularly: GPU musings (with an eye on genomics) - HackMD
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I am also very interested in finding a “sweet spot” in terms of price vs performance for GPUs when being used for basecalling. Here is a document where I have started some benchmarking and will keep updating with additional GPUs and information: GPU price / performance comparisons for Nanopore basecalling - HackMD
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If you are interested in what it looks like if you run windows I have a quick note on that (spoiler: use Linux!): Nanopore Guppy GPU basecalling on Windows using WSL2 - HackMD
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For the last 2-3 years it has been a project of mine getting Nanopore sequencing and software running on Nvidia Jetson devices (ARM based devices in general). This has been highly successful, and I maintain a GitHub repo with notes and instructions: GitHub - sirselim/jetson_nanopore_sequencing: A place to collate notes and resources of our journey into porting nanopore sequencing over to accessible, portable technology.
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If you are interested in using free GPUs in the cloud, we have a guide to do this using Google Colab: My notes on setting up basecalling on Google Colab · GitHub
OK, so that’s an overview of some hopefully useful bits and bobs. I would now like to comment on a few things. Firstly, you really want to hold on to your fast5 files, doing so allows you to return to them again and again as models improve accuracy and allow the deteciton of additional base modifications. Real-time basecalling while sequencing is awesome, and something like an RTX3060 can keep up easily in high accuracy mode (HAC), even in super high accuracy (SUP) with some tweaking. But you will always want to go back and basecall again after the fact. The Jetson Xavier AGX will not keep up with HAC calling in real-time (we’ve tried), but in FAST mode it’s great, you can actually run 2x MinIONs. The Clara AGX could easily keep up, but it’s not widely available yet. While the A10 is an amazing card, I would advise to spend that amount of money on other things. Something like a 308Ti or a 3090 is more than enough for 95% of people (probably 99.9% of people to be honest).
Sorry for the long post, happy to comment more if useful.
-Miles