January 12, 2021 — Oxford Nanopore Technologies and Nvidia are collaborating this year to integrate the Nvidia DGX Station A100 into Oxford Nanopore’s gene sequencing system, PromethION with the aim of delivering real-time analyses at scale, and can also analyze any length fragment of DNA/RNA.
“The use of accelerated computing and artificial intelligence to quickly and accurately sequence DNA or RNA supports the increasing availability of nanopore sequencing data, at scale, to a variety of high-throughput users,” Oxford Nanopore said in its announcement. “Oxford Nanopore’s technology is increasingly being used by scientific researchers analysing many thousands of genomes to better understand genetic diversity and discover new variants. Sequencing is also being increasingly adopted to generate rapid insights in healthcare settings, food safety, or environmental analysis.”
Nvidia’s 2.5 petaFLOPS DGX Station A100, announced in November, is a data-center-grade, GPU-powered, multi-user workgroup appliance built for AI workloads. It plugs directly into a wall outlets and is quiet, according to Nvidia, because of its refrigerant-based cooling system. It contains four A100 80GB GPUs connected via Nvidia NVLink, to offer 320GB of GPU memory.
Oxford Nanopore’s PromethION P48 sequencing device generates as much as 10 Terabases of DNA information per 72-hour run (sufficient to analyse 96 human genomes at 30X coverage). Achieving the 10 Terabase run barrier was announced in December and represents a 25 percent increase in data output compared to its previous best earlier last year. This increase has been driven by improvements in flow cell chemistry, many of which were included in new shipments from mid-November 2020. These developments have been reflected in customer data, with increasing yields reported across a range of sequencing applications.
“Supplied in a P24 and a P48 format, PromethION is increasingly being deployed into high-throughput projects, where the rich sequencing data provided by Oxford Nanopore can be delivered at very high throughput,” the company said. “As with all Oxford Nanopore devices, the technology enables academic groups, core facilities and service providers to realise the value of sequencing any length fragments, from short fragments to those that are over 100,000 bases long, and to characterise base modifications, coupled with high accuracy single nucleotide or structural variant calling and phasing.”
Nvidia GPUs are already used in other Oxford Nanopore sequencing systems, driving real-time sequencing analysis at any scale. The desktop GridION includes NVIDIA V100 technology and the handheld MinION Mk1C sequencer is powered by the NVIDIA Jetson Edge AI platform.
source: Oxford Nanopore