Nanopore sequencer analysis machine (May 2023 version) | Information dissemination media for research and development TEGAKARI

Case No.PC-10347BA customer who saw this consulted us about considering a PC for a similar purpose.
In addition to nanopore sequencer analysis, we are planning to use the software "DeepVariant" using DeepLearning, and we would like the following configuration.

・CPU: AMD Threadripper
・ Memory: 128GB
・Storage: SSD (NVMe is not required)
・ GPU: RTX4090

・Software used: Guppy, Dorado, DeepVariant

Based on the conditions you contacted us, we proposed the following configuration.

【Main Specifications】

CPU	AMD Ryzen ThreadripperPRO 5965WX (3.80GHz 24 cores)
memory	128GB REG ECC
storage	2TB M.2 SSD
Video	NVIDIA Geforce RTX4090
network	on board (1GbE x1 10GBase-T x1)
Housing + power supply	Tower type housing + 1200W
OS	Ubuntu 20.04

The estimate is for a configuration that uses Threadripper for the CPU.
At the time of your proposal, the conventional Threadripper series was discontinued, so the configuration is equipped with Threadripper Pro.
The cost of the CPU is high, but the CPU performance is high and you can use it all-round.

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 Nanopore?
A nanopore is a nanometer (nm) sized pore.The nanopore sequencer uses an artificial membrane protein with nanopores and determines the base sequence from changes in the electric current when DNA passes through the nanopores.Nanopore sequencers are characterized by the ability to analyze longer-read DNA than conventional next-generation sequencers.

・What is Guppy?
Guppy is a genetic information display program that graphically displays gene sequence data.Regions in the sequence that are translated into proteins and annotations for sites known as markers can be displayed or edited in an easy-to-understand manner.

・What is Dorado
Dorado is a genetic analysis software used to assemble and annotate RNA-seq data generated by nanopore sequencing.At the time of publication of this example, it was released in the alpha version, not the full version.
RNA-sequencing data can be used to assemble high-quality sequences for accurate transcript identification and annotation, thus optimizing for short read lengths and high error rates, which are challenges in nanopore sequencing. It can be said that it is done.

reference:nanoporetech/dorado *Jumps to an external site

・What is Deep Variant?
DeepVariant is genome analysis software that utilizes DeepLearning to detect high-quality genomic mutations.Convolutional neural networks are used for genomic analysis to detect base mutations in DNA.
It is provided as open source and is used in various fields such as genome research, medical field, and genetic counseling.