MinKNOW software installation doubt for MinION Nanopore sequencing
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3 months ago
Soumajit ▴ 40

Hi good people,

Recently in lab we have received a Nanopore MinION device and currently trying to figure out installation and other details. I am seeking a few suggestions from users and experts.

  1. The running machine spec is AMD Ryzen 9 7900 12-core processor, 64GB memory running a Windows OS and also consists NVIDIA GeForce RTX 4060 TI. Based on this could you kindly suggest should I install the CPU and GPU version of the MinKNOW software to have optimum performance?

  2. I have experience with command-line and Linux. Is it better to use the MinKNOW through Ubuntu? What are some pros and cons of doing that over using GUI?

  3. If I understood correctly the new MinKNOW software have integrated basecaller (Dorado) onboard already. Then do I have to install in again locally for basecalling purpose?

Initially I am planning to sequence viral RNA (not directly. through cDNA prep and ligation sequencing kit), later on once I establish the protocol, would move over to mammalian cell transcriptome.

Would be really helpful to have some suggestions. Thanks a lot. Love.

MinKNOW MinION Nanopore • 502 views
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Based on this could you kindly suggest should I install the CPU and GPU version of the MinKNOW software to have optimum performance?

Use GPU version is your GPU is supported. It will always be faster than CPU.

If I understood correctly the new MinKNOW software have integrated basecaller (Dorado) onboard already. Then do I have to install in again locally for basecalling purpose?

Looks like it. So you will not need to install Dorado separately.

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