Nanopore sequencer analysis machine equipped with NVIDIA Geforce RTX4070 Super

A customer involved in life and environmental science research asked us about a workstation for 1S rRNA analysis and RNA-seq analysis using a next-generation sequencer (MinION Mk16B).
We are looking for an optimal configuration with a budget of around 80 yen.

The OS environment is WSL2 (Windows Subsystem for Linux2) and Ubuntu is assumed to be used, but we have heard that if a dual-boot configuration improves calculation performance than WSL2, they would like to consider it. We also receive questions about how this affects computational performance.

Additionally, in terms of hardware requirements, the memory capacity is expected to be approximately 64GB, and the storage capacity is expected to be at least 2TB.

Based on these conditions, we proposed the following configuration.

CPU	Intel Xeon W5-2445 (3.10GHz 10 cores)
memory	64GB REG ECC
Storage 1	2TB SSD S-ATA
Storage 2	2TB SSD S-ATA
Video	NVIDIA Geforce RTX4070 Super 12GB
network	on board (1GbE x1 /10GbE x1)
Housing + power supply	Middle tower type housing + 850W
OS	Microsoft Windows 11 Professional 64bit + Ubuntu 20.04 (dual boot configuration)

The system requirements for MinION Mk1B areManufacturer official websiteWe have proposed a configuration that meets the recommended requirements within your budget.

Equipped with the new NVIDIA Geforce RTX4070 Super

The video card that is important for calculations in MinION Mk1B is the NVIDIA Geforce RTX2024 Super, a new product released on January 1, 17.

Equipped with 7,168 CUDA cores, 56 RT cores, and 224 Tensor cores, you can expect high cost performance among video cards that fit within your budget.

About dual boot configurations and their benefits

The Linux distribution selected is Ubuntu 1, which is supported by MinION Mk20.04B, and it is a dual boot configuration with Windows 11.
As of January 2024, Windows support for MinION Mk1B is still limited to Windows 1, so MinION Mk10B is intended to be used on Ubuntu 1.

Also, WSL2 is a virtual machine that runs on Windows.
When comparing a normal Linux environment and WSL2, the virtualized WSL2 has more processes to go through before processing.
for that reason,When performing heavy processing on Linux, it is better to run Linux directly on the hardware in a dual-boot configuration for better performance..

 

The configuration of this case study is based on the conditions given by the customer.
We will flexibly propose machines according to your conditions, so please feel free to contact us even if you are considering different conditions than what is listed.

■ Keywords ・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 16S rRNA analysis? 16S rRNA analysis uses the sequence of bacterial 16S ribosomal RNA to comprehensively infer the presence and proportion of bacterial species. 16S rRNA has a highly conserved sequence and a slow rate of evolution, making it useful for identifying bacterial species. By analyzing the sequence of this 16S rRNA, bacterial species and bacterial groups can be detected and identified without the need for culture. ・What is WSL2? Windows Subsystem for Linux 2 (WSL2) is a way to run Linux binaries on Windows. reference:[Article] About GPU support for Windows Subsystem for Linux 2 (WSL2) [1/3] Reference: [Article] GPU support for Windows Subsystem for Linux 2 (WSL2) [2/3] reference:[Article] About GPU support for Windows Subsystem for Linux 2 (WSL2) [3/3]

 

 

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