Workstation for Omics analysis | TEGAKARI, an information dissemination media for research and development

A customer involved in research in the life sciences field contacted us to inquire about replacing the bioinformatics workstation they were currently using.
The condition is that SAMtools and STAR, which are used for basic Omics analysis, and Higlass, which is used to visualize Hi-C data, must be able to be operated smoothly, and the client would like to consider a configuration with specifications equal to or better than the PC they are currently using, within a budget of 80 to 160 million yen.

We have heard that you are currently using a PC with the following specifications:

CPU	Intel Xeon E5-2640 v4 ×2 (20 cores/40 threads)
memory	256GB REG ECC
Video	NVIDIA Quadro P620
OS	Ubuntu 22.04

Taking these requests into consideration, we proposed the following configuration:

CPU	Intel Xeon Gold 5418Y (2.00GHz 24 cores) ×2
memory	256GB REG ECC
storage	4TB SSD M.2 NVMe Gen4
Video	NVIDIA T1000 8GB
network	on board (10GBase-T x2)
Housing + power supply	Middle tower type housing + 1000W
OS	Ubuntu 22.04

Configuration that prioritizes CPU specifications within your budget

This configuration is tailored to your budget and has higher specs than your current machine.

The CPU is equipped with two Xeon Gold 5418Y, achieving 2 cores, more than double the number of the current machine (20 cores).

The memory capacity is 256GB, the same as the current machine, but there are eight free memory slots, allowing for future memory expansion.

Considering that the storage capacity will be for analytical purposes, a 4TB M.2 NVMe Gen4 SSD was selected to provide ample storage capacity.
Because this is an NVMe-connected product, you can expect faster data read/write speeds compared to SATA-connected HDDs or SSDs.

With a total of 48 CPU cores and 256GB memory capacity, you can expect rapid processing even for bioinformatics analyses, which tend to require large amounts of calculations.

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 Omics analysis?
Omics analysis is a data-driven approach widely used in biology and medicine. Omics is a general term for technologies for collecting and analyzing biological data, such as genomics, proteomics, and transcriptomics.
Omics analysis utilizes advanced technologies such as high-throughput experimental techniques and next-generation sequencing.The large amount of data generated by this is analyzed using statistical techniques and data mining techniques, enabling analysis of disease mechanisms, identification of new biomarkers, and application to personalized medicine.

・What is the Hi-C method?
This whole genome analysis method is an advanced version of the 3C (Chromosome Conformation Capture) method. It uses a next-generation sequencer to comprehensively detect pairs of genomic DNA fragments that are spatially adjacent in the three-dimensional genome structure within the cell nucleus, and can estimate and analyze the three-dimensional genome structure.

・What is Samtools?
Samtools is a group of programs for manipulating data output from next-generation sequencers.
Samtools　(read/write/edit/index/view SAM/BAM/CRAM format)
BCFtools (read/write BCF2/VCF/gVCF files and call/filter/summarize SNP and variant data)
HTSlib (AC library for reading/writing next-generation sequencing data)

Reference: Samtools (Genome Research Limited) *Jump to external page

What is STAR?

STAR is a program that maps reads (raw data) obtained by RNA-Seq to reference sequences. It is available on Github, and although it requires high specifications, it has a fast mapping speed.

reference:alexdobin/STAR | GitHub *Jump to external page

・What is HiGlass?

HiGlass is a data viewer that allows fast visualization of large-scale Hi-C and other genomic data sets, enabling exploratory data analysis in conjunction with other omics data.