Next-generation sequencer analysis workstation | Information dissemination media for research and development TEGAKARI

A customer involved in research in the bioinformatics field asked us about a workstation for performing next-generation sequencer analysis.
The software used in the analysis pipeline is scheduled to be "BWA", "GATK", "Samtools", etc., and the desired conditions are as follows.

・CPU: 32 threads or more
・Memory: Equipped to the limit within the budget (planned to expand up to 1TB in the future)
・Storage: 512GB to 1TB SSD NVMe type
・GPU: OK if the screen can be displayed
・OS: No installation (scheduled for ubuntu 20.04)

・Budget: About 120 million yen

Based on the conditions, we proposed the following configuration.

【Main Specifications】

CPU	AMD Ryzen ThreadripperPRO 5965WX (3.80GHz 24 cores)
memory	256GB REG ECC
Storage 1	1TB M.2 SSD
Video	NVIDIA GeForce GT710
network	on board (1GbE x1 10GBase-T x1)
Housing + power supply	Tower type housing + 1000W
OS	None

The CPU uses Ryzen ThreadripperPRO 5969WX (24 cores 48 threads).
The storage is NVMe type 1TB SSD.

It has 256GB of memory and can be expanded up to 1TB.
However, the memory module configuration at the time of shipment is 64GB x 4, and considering that there are 4 empty memory slots, it is difficult to achieve 1TB just by adding more.
If you want to make use of the memory in the initial state, you can add 64 x 4GB and expand it to 512GB.
When expanding to 1TB, it is necessary to remove the existing 64GB module and install x128 8GB modules.

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 BWA?
BWA is a software package for mapping low divergence sequences against large reference genomes such as the human genome. It consists of three algorithms: BWA-backtrack, BWA-SW, and BWA-MEM.

reference:Burrows-Wheeler Aligner *Jump to external page

・What is GATK?
GATK (Genome Analysis Toolkit) is a group of analysis tools for analyzing variants (gene mutation analysis) from nucleotide sequence data output from next-generation sequencers.The contained tools can be used individually or in conjunction.

reference:Genome Analysis Toolkit (Broad Institute) *Jump to external page

・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