Machine for NGS analysis & nanopore sequencer analysis

A customer who was planning to perform simple NGS analysis and nanopore sequencer analysis consulted us about the introduction of a dedicated machine.
Specifically, it is used for hybrid assembly of about 30Mb using MaSuRCA and for RNA-seq analysis.
We are also considering using the GPU version of Guppy basecaller, but other 3D model processing is not planned.

The OS is assumed to be Ubuntu, but we have heard requests to run Ubuntu on Windows if using it with WSL does not significantly affect the analysis performance.

Other assumptions are as follows.

・CPU: A product with about 12 cores is assumed, but if there is a better proposal, I would like it ・Storage: I want SSD ・Budget: About 50 million yen ・On the MaSuRCA download page, there is a description of "Bacteria (up to 10Mb): 16GB RAM, 8+ cores, 10GB disk space" as a hardware requirement, so if it is 30MbPC 10596I think that it will work with the specs of about

Based on the conditions you contacted us, we proposed the following configuration.

【Main Specifications】

CPU	AMD Ryzen9 7950X (4.50GHz 16 cores)
memory	64GB
storage	2TB SSD S-ATA
Video	NVIDIA Geforce RTX3060
network	on board (2.5G x1 10/100/1000Base-T x1) Wi-Fi x1
Housing + power supply	Middle tower case + 850W
OS	Ubuntu 20.04

Although the specifications are provisional, they are intermediate specifications between Bacteria and Insect, which are the operating requirements posted on the official MaSuRCA repository.

reference:alekseyzimin / masurca *Jumps to an external site

It is assumed that only Ubuntu is installed as the OS.
Regarding use with WSL, the software itself seems to work, but the analysis performance is unavoidably affected.
WSL is essentially a virtual machine, so there is some virtualization overhead. Unless you have no other reason to have Windows, I recommend running Ubuntu natively.
Another option is to build a dual boot environment for Windows and Ubuntu.Please contact us if you are interested.

In addition, this configuration is equipped with an NVIDIA video card and supports GPU execution of Guppy.

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 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. reference:GUPPY gene information display program (National Institute of Advanced Industrial Science and Technology) *Jumps to an external site   ・What is MasuRCA? MaSuRCA is software for genome assembly that specializes in hybrid assembly of high-quality paired-end reads and long reads.Data from different read types can be combined to produce fast and accurate assemblies. reference:alekseyzimin / masurca *Jumps to an external site   ・What is hybrid assembly? Hybrid assembly is a method of genome assembly that combines data from different read types.Using both short paired-end reads and long reads can improve assembly accuracy and continuity.   ・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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