Transcriptome analysis machine | Information dissemination media for research and development TEGAKARI

A customer involved in research on developmental biology asked us for a Linux machine that can perform a series of data analyzes (preprocessing, mapping, DEGs calculation, etc.) on rice transcriptome and genome data without complaint.
Your requirements are as follows.

・CPU: CPU with 24 cores and 48 threads or more
・ Memory: 256GB
・Storage: SSD 1TB
・OS: Linux

The transcriptome analysis of rice is approximately 1 Gbp in size, and the whole genome resequencing analysis is approximately 10 Gbp in size.

During the examination, we asked questions and consulted on the following two points.

・The CPU is assumed to be Xeon, but how should performance and cost be considered compared to AMD Threadripper?

・The OS is scheduled to be Ubuntu or Rocky Linux, but which distribution is suitable for Linux beginners?

Based on the above information, we would like to propose a budget of 90 yen or less.

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

【Main Specifications】

CPU	Xeon Silver 4310 (2.10GHz 12 cores) x2
memory	256GB REG ECC
storage	1TB SSD S-ATA
Video	Nvidia T400
network	On Board (1000Base-T X2)
Housing + power supply	Tower type housing + 850W
OS	Ubuntu 22.04

With a 3 CPU configuration equipped with 2rd generation Xeon Scalable, the system has a total of 24 cores/48 threads.

■ Storage

Although the genome size of rice is not that large compared to that of humans, the volume of analysis data is considered to be quite large.In this case, we have heard that the customer will prepare an external storage for data storage, but if you are using only the PC itself, we recommend that you install a storage for data.

■ CPU

When comparing 24-core Xeon and Threadripper PRO, Threadripper PRO is superior in terms of performance.
In terms of the price of a single CPU, ThreadripperPRO is relatively cheaper than Xeon, but in terms of the total cost of the entire configuration, the ThreadripperPRO 24-core configuration is in the first half of the million yen range, so in this case, we prioritized cost and made it cheaper. We are proposing a Xeon 100 CPU configuration.

Since the number of CPU cores and memory capacity is important for next-generation sequencer analysis, it is not very effective to increase the calculation speed by reducing the number of cores and focusing on the clock.Therefore, even if the single-core performance is somewhat low, please think that it is desirable to give priority to the configuration that can secure the number of cores.

■OS

When it comes to OS, Rocky Linux is less flexible than Ubuntu.
This is due to the difference in development philosophy between Ubuntu and Rocky Linux (Redhat Enterprise Linux on which it is based).

Rocky Linux is based on RHEL, which puts long-term operational stability first.
Ubuntu is excellent as a distribution for workstations, and if you value performance as a workstation with the latest hardware, there are advantages in terms of package update frequency, kernel version, etc.

If you don't have a strong reason to choose Rocky Linux, we recommend Ubuntu.

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 transcriptome analysis?
Transcriptome refers to the entirety of gene transcripts (mRNA) in tissues and cells.Transcriptome analysis is an analysis method for comprehensively understanding the expression status of genes in living cells. Also called RNA-Seq analysis or gene expression analysis.

・What is Ubuntu?
Ubuntu is a Linux distribution.It is provided as free software and can be easily installed and used in a short time using a graphical installer.

reference:Ubuntu (Ubuntu Japanese Team) *Jumps to an external site

・What is Rocky Linux?
Rocky Linux is a Linux distribution. It uses the source code of Red Hat Enterprise Linux (RHEL) and is compatible.It is provided as free software and features stability through long-term regular updates.

reference:Rocky Linux (Rocky Enterprise Software Foundation) *Jumps to an external site