A machine for analyzing NGS data acquired with the Nextseq2000 system | TEGAKARI, an information dissemination media for research and development

A customer involved in the research and development of biopharmaceuticals asked us about a machine for analyzing NGS data acquired by the Nextseq2000 system.
Your requirements are as follows.

・CPU: Intel Xeon 24 core or more x2
・Memory: About 768GB
・Storage 1: SSD 2TB M.2
・Storage 2: HDD 4TB S-ATA
・OS: Ubuntu
・Budget: As close as possible to 200 million yen

We proposed the following specifications as a configuration that satisfies the requested number of CPU cores.

CPU	Xeon Gold 6338 (2.00Hz 32 cores)
memory	512GB
Storage 1	2TB M.2 SSD
Storage 2	8TB HDD S-ATA
video	on board (VGAx1)
network	On Board (1000Base-T X2)
Housing + power supply	Tower type housing + 850W
OS	Ubuntu 22.04

The CPUs are selected so that each CPU has 1 cores x 28 for a total of 2 cores.

The 3rd Gen Xeon Scalable has 8 memory channels, so if you want more than 768GB and the optimal configuration, you should choose 1TB.
However, in that case, the budget would be greatly exceeded, so for the time being, we proposed a 512GB with an optimized module configuration with a smaller capacity than desired, and we decided to check the specifications and price.

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 HISAT2?
HISAT2 is an alignment program for mapping reads (both DNA and RNA) in next-generation sequencing to a population of human genomes and a single reference genome.Fast and low memory usage.

reference:HISAT2 *Jumps to an external site

・What is Bowtie2?
Bowtie2 is a tool for aligning sequence reads to reference sequences.It excels at aligning relatively long genomes such as those of mammals.

reference:Bowtie2 *Jumps to an external site

・What is Samtools?
Samtools is a suite of programs for working with high-throughput sequencing data. It consists of three independent repositories: "Samtools", "BCFtools" and "HTSlib".

reference:Samtools *Jumps to an external site

・What is Velvet?
Velvet is a program for assembling genome sequences. A tool for de novo assembly based on de Bruijn graphs, suitable for short read data with high coverage.Also, by manipulating the de Bruijn graph, algorithms are implemented to eliminate sequence errors and eliminate repeats.

reference:Velvet *Jumps to an external site

■ Click here for details and inquiries about this PC case
A machine for analyzing NGS data acquired with the Nextseq2000 system