Bacterial NGS analysis workstation

A customer involved in bioinformatics contacted us regarding an NGS analysis workstation for individual researchers.
The OS will be Ubuntu, and the software to be used will be GROMACS, Spades, and Unicycler. They are hoping for a configuration that can handle MD calculations that will be performed several times a year.
The budget is around 100 million yen, and the design requires emphasis on memory and storage expandability, as well as the ability to accommodate future GPU additions.

CPU	Intel Xeon 6505P 2.20GHz (up to 4.10GHz at TB3.0) 12C/24T x2 configuration
memory	Total 128GB DDR5 5600 REG ECC 16GB x 8
Storage 1	4TB SSD M.2 NVMe Gen4
Storage 2	4TB HDD S-ATA (Life Science Campaign Bonus 1)
Video	On Board (VGA x1)
network	on board (10GbE x2)
Housing + power supply	Mid-tower chassis + 1500W 80PLUS PLATINUM
OS	Ubuntu 24.04

This configuration is an example of applying the benefits (4TB internal HDD storage service) of the currently ongoing "Special Campaign for Life Science Research and Development."
Click here for details of our special campaign for life science R&D

About CPU

To maximize the multi-threaded performance of SPAdes and GROMACS, we secured as many cores as possible within our budget.
By using two Xeon 6505P (12 cores) for a total of 24 cores, we have created an environment that is strong in parallel processing.

About memory

The memory is 128GB (8 x 16GB).
You can expand the memory by using an available slot to add up to 256GB, and you can increase the capacity even further by upgrading to a higher-spec memory.

Storage Configuration

A 4TB M.2 SSD is installed for high-speed access, and a 4TB HDD is also added for large-capacity data storage.

GPU selection and scalability

At present, the system is configured with an onboard GPU, assuming CPU analysis, but the chassis is designed to accommodate future addition of a GPU for GROMACS.
There is also ample power capacity, allowing for flexible upgrades.

For those who are active in these fields Bioinformatics Molecular dynamics Genome analysis Life Science Computational Chemistry

Tegara's custom-made PC production service not only caters to initial use, but also supports system expansion in anticipation of future expansion of research scale.
We not only propose configurations that meet various software requirements, but also accept consultations regarding the construction of an entire research environment.
Please feel free to contact us and we will provide the best solution to suit your needs.

Keyword What is SPAdes? SPAdes is an open-source assembler for microbial and transcriptome analysis. It supports hybrid assembly centered on short reads and is widely used for bacterial genome draft generation, plasmid analysis, single-cell analysis, etc. reference:SPAdes Genome Assembler *Jumps to an external site What is a Unicycle? Unicycler is a hybrid assembler that combines short and long reads to achieve high-precision assembly of bacterial genomes and plasmids. Its unique feature is that it automatically performs k-mer optimization and polishing while internally using SPAdes, making it easy to complete circular sequences even with a small number of long reads. reference:Unicycler · GitHub *Jumps to an external site What is GROMACS? GROMACS is open source software that can perform molecular dynamics simulations on a scale of hundreds of thousands to millions of atoms at high speed. It supports advanced parallel calculations using GPUs and multi-core CPUs, allowing for efficient large-scale, long-term analysis. reference:GROMACS Official Website *Jumps to an external site

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