Oxford Nanopore upgrades the PromethION compute tower to increase power and capacity

Oxford Nanopore has announced it will upgrade its PromethION compute tower from NVIDIA’s V100 to A100 technology, this processing power increase will enable it to keep up with high accuracy basecalling and greatly expand the capacity for super accuracy algorithms

PromethION upgrades

All orders placed from today for Oxford Nanopore’s PromethION will contain four NVIDIA A100 Tensor Core GPUs. Internal benchmarks have shown an increase in basecalling speed performance of over 50% when using A100, compared to previous hardware. Additional early benchmarks on NVIDIA’s just announced H100 Tensor Core GPU, which show significant future improvements and work is ongoing to ensure these can be introduced into the PromethION range in the near future.

Oxford Nanopore’s in-house algorithm teams continue to work closely with industry partners to develop improvements to both the speed and the accuracy of the neural networks. When combined with the latest chemistries, this will deliver over 99% raw read accuracy and duplex accuracies approaching 99.9%.

Rosemary Sinclair Dokos, VP Product and Programme Management commented:

“We have been working closely with NVIDIA to further accelerate the data analysis pipeline offering. This we believe will pave the way for fully integrated ‘sample to answer’ workflows at scale on PromethION.”

Increasing the capacity of onboard analysis of the PromethION devices will simplify the workflow for nanopore users who are delivering large sequencing projects at speed, whilst also enabling the analysis of all variant classes including single-nucleotide variants (SNVs) and structural variations (SVs), as well as methylation. Remora, Oxford Nanopore’s latest methylation detection software is being integrated into MinKNOW to provide this information in parallel during the sequencing run.

All orders placed from today will contain the new technology, there has been a pricing change to reflect the additional cost of the new technology, and they will be available to customers from May onwards. Additionally, there are upgrade plans to roll this out to users who have existing devices. See our store for PromethION packages.

High throughput sequencing with the PromethION

To date, teams have successfully carried out high throughput sequencing projects using the PromethION device and this update will enable further progress at this scale.

A team generated long-read sequencing data, using Oxford Nanopore’s PromethION, from 3,622 Icelanders to study the potential of the tech to improve the characterisation of structural variants (SVs). From this data, they identified a median of 22,636 SVs per individual and were able to explore their effects on diseases and other traits. The results show that SVs can be accurately characterised at the population scale using nanopore tech in a genome-wide, non-targeted approach, and demonstrate how SVs impact phenotypes. Full paper available here.

The tomato is one of the most valuable agricultural crops in the world, so Michael Schatz and colleagues sequenced 12–16 samples per week, using the PromethION platform, to achieve a target of 100 genome sequences in 100 days. Such large-scale sequencing efforts enabled the rapid and high-throughput genome-wide characterisation of a wide variety of tomato species, and can potentially provide the genetic information needed to enrich for desired genome traits and increase the efficiency of crop breeding in the future. More information available here.

Nanopore technologies can sequence short to ultra-long fragments of DNA, making it easier to obtain more complete genome assemblies. Based on this, a team set out to generate a chromosome-scale assembly of a banana genome using Oxford Nanopore long-reads. They generated a genome coverage of 177X from a single PromethION Flow Cell. From the 11 chromosomes, five were entirely reconstructed in a single contig from telomere to telomere, revealing for the first time the content of complex regions like centromeres or clusters of paralogous genes. Full paper here.