Nanopore sequencer analysis machine (GPU performance priority) | Information dissemination media for research and development TEGAKARI

A customer inquired about a machine for long-chain DNA analysis using a nanopore sequencer.
The assumed conditions are as follows.

・CPU: 2 CPU configuration is desirable
・Memory: About 64GB
・Storage: Use NAS for SSD data storage area of 2TB or more
・GPU: NVIDIA RTX2060 or higher I want the GPU with the highest performance within the budget
・OS: Ubuntu will be installed (hoping to ship without OS)
・Budget: About 90 million yen

Based on the information you provided, we proposed the following configuration.

【Main Specifications】

CPU	Xeon Silver 4314 (2.40GHz 16 cores)
memory	64GB REG ECC
storage	2TB M.2 SSD
Video	NVIDIA Geforce RTX4090
network	On Board (1000Base-T X2)
Housing + power supply	Middle tower case + 1200W
OS	None

When considering the configuration, the key point is the conditions related to the CPU and GPU.
Considering the budget, it is difficult to satisfy both conditions at the same time.
The configuration that prioritizes the 2CPU configuration isCase No.PC-10347A .

The RTX4090 GPU has better performance than the RTX2060 in terms of both generation difference and product grade.
However, due to the physical size of the GPU and the need to exhaust heat, it is not possible to add more GPUs in the future.

The configuration of this case study is based on the conditions given by the customer.
Please feel free to contact us even if you are considering different conditions from what is posted.

■FAQ

・What is Nanopore?
A nanopore is a nanometer (nm) sized pore.The nanopore sequencer uses an artificial membrane protein with nanopores and determines the base sequence from changes in the electric current when DNA passes through the nanopores.Nanopore sequencers are characterized by the ability to analyze longer-read DNA than conventional next-generation sequencers.

・What is MinKNOW?
Dedicated software for sequencing with the nanopore sequencer "MinION".
The MinION itself is a sequencer that connects directly to a PC via USB, and requires a certain level of machine specs.

reference:Laboratory and IT Requirements (Oxford Nanopore Technologies) *Jumps to an external site

・What is Guppy?
Guppy is a genetic information display program that graphically displays gene sequence data.Regions in the sequence that are translated into proteins and annotations for sites known as markers can be displayed or edited in an easy-to-understand manner.