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Learn about all of the new applications, features, and functions released for developers to build, extend, and connect 3D tools and platforms to the Omniverse ecosystem seamlessly.

Developers, creators, and enterprises around the world are using NVIDIA Omniverse—the real-time collaboration and simulation platform for 3D design—to enhance complex workflows and develop for 3D worlds faster. At NVIDIA GTC, we showcased how the platform’s ecosystem is expanding, from new Omniverse Connectors and asset libraries to updated Omniverse apps and features.

With these latest releases and capabilities, Omniverse developers can build, extend, and connect 3D tools and platforms to the Omniverse ecosystem more easily than ever before.

Omniverse Kit 

Omniverse Kit is a powerful toolkit on which Omniverse applications are built.

The latest version includes core functionality and rendering improvements for 3rd party renderer integrations and Arbitrary Output Variables (AOV) support.

Key updates:

• Manipulator Framework: Create 3D manipulators within the viewport.
• Hydra Delegates: Add hydra-based renderers to Kit based applications.
• WARP in Omnigraph: Create GPU-accelerated Omnigraph compute nodes using Python syntax.
• MDL Python Support Added: Enhance ability to integrate MDL through Python.

Omniverse Nucleus

Omniverse Nucleus Workstation and Enterprise Nucleus Server were updated with a new navigator and several features requested from the community.

Key feature:

• DeepSearch, a new AI-based search microservice for Nucleus. Users can search through massive, untagged databases of assets using natural language or images. Now available for early access to Omniverse Enterprise customers.

Omniverse Cloud

At GTC, we announced Omniverse Cloud, a suite of cloud services that provide instant access to the NVIDIA Omniverse platform. Omniverse Cloud encompasses several services, including Nucleus Cloud, now in early access, plus Omniverse Create and View apps streaming from the cloud.

Omniverse Apps 2022.1 updates

Omniverse Create 

With Omniverse Create advanced scene composition users can interactively simulate, and render scenes in Pixar USD in real time.

Key updates:

• General animation keyframing and curve editing.
• ActionGraph based on Omnigraph to map keyboard shortcuts and your own user interface buttons. 
• New PhysX GPU accelerated softbody support.
• vMaterials 2.0 additions. Access a massive library of over 900 physical materials.
• Animation Graph (beta): Bring characters to life with our new node-based graph editor for runtime animation blending and playback.

Omniverse View

With Omniverse View, project reviewers can collaboratively review 3D design projects in stunning photorealism. 

Key updates releasing March 30:

• Markup: Add editable text, shapes, and scribbles to convey comments. 
• Measure: A variety of snapping methods are available to measure between entities and create desired dimensions.
• Turntable: Rotate objects on a virtual turntable to see how light affects the model.
• Teleport: Move around large scenes by jumping great distances to place the camera in an area.
• Waypoints 2.0: Edit or reorder waypoints, and easily create a 3D slide deck walkthrough.

Omniverse Machinima

With Omniverse Machinima, users can collaborate in real time to animate and manipulate characters and their virtual world environments. 

Key updates:

• Track and capture motion in real time using a single camera, with live conversion from 2D camera capture to 3D model in the Maxine Pose Estimation workflow.
• Faster and easier to use sequencer with tools such as splitting, looping, hold, and scale, and even more “drag and drop” functionality.
• Animation Retargeting (beta): Easily remap skeletal animations from one biped to another, with presets for popular character systems like Reallusion Character Creator 3.

Omniverse XR App

Coming soon to beta, the new Omniverse XR App lets you bring your 3D work into human scale. View, review, and annotate Omniverse scenes, manipulate 3D objects, control the lighting all in VR. 

New developer tools

Omniverse Code

Omniverse Code is the integrated development environment that helps developers build Kit-based extensions, apps, and microservices easier than ever.  Key features, releasing March 30, include new interactive documentation and templates along with Omniverse Replicator extensions.

Omniverse Replicator

NVIDIA Omniverse Replicator is a framework built on the Omniverse platform that enables physically accurate 3D synthetic data generation to accelerate training and accuracy of perception networks. Omniverse Replicator is now available as a set of Omniverse Extensions, with content, and examples within Omniverse Code App in the Omniverse Launcher.

Omniverse Avatar

NVIDIA Omniverse Avatar, a technology platform for generating interactive AI avatars, connects NVIDIA technologies in speech AI, computer vision, natural language understanding, recommendation engines, and simulation technologies. While currently under development, developers and artists can get started with one piece of the Avatar technology, Omniverse Audio2Face. 

Partner ecosystem updates

New support for the Omniverse ecosystem provided by leading 3D marketplaces and digital asset libraries gives creators an even easier way to build their scenes. TurboSquid by Shutterstock, Sketchfab, Twinbru, and newly added Reallusion’s ActorCore assets are searchable directly inside the Omniverse App asset browser. Joining our catalog of Omniverse-ready assets alongside CGTrader is A23D, bringing 40,000 Omniverse-ready assets to users.

New Omniverse connections

• Adobe Substance 3D Material Extension: Import Substance 3D asset files into any Omniverse App.
• Adobe Substance 3D Painter Connector: Apply textures, materials, and masks or UV mapping onto 3D assets with Adobe Substance 3D Painter, releasing March 28.
• Unreal Engine 5: Send and sync model data and export Nanite Geometry to Omniverse Nucleus.
• e-on VUE: Create beautiful CG environments including skies, terrains, roads, and rocks.
• e-on PlantCatalog: Export a plant, enable live-sync, and edit in real time. 
• e-on PlantFactory: Create ultra-realistic, high polygon plants.
• Maxon Cinema 4D: USD is now supported. Use the app in a connected workflow with OmniDrive. 
• Ipolog: Perform material provisioning and production logistics for manufacturing planners.  
• LumenRT for NVIDIA Omniverse, powered by Bentley iTwin: Allows engineering-grade, millimeter-accurate digital content to be visualized on multiple devices and form factors.

Supported Hydra renderers

Creators, designers, and developers can now integrate their favorite Hydra delegate renderers directly into their Omniverse workflows by building a Hydra render delegate themselves or using NVIDIA-built Hydra render delegates for Pixar HDStorm, Maxon RedShift, and OTOY Octane, with Blender Cycles, Chaos V-Ray, and Autodesk Arnold coming soon.

New CAD Importers

Manufacturing and product development workflows just became easier with the introduction of 26 CAD Importers to Omniverse. Developers, designers, and engineers can now easily bring in common CAD formats from leading ISV applications directly into Omniverse.

Explore more at GTC  

Join Omniverse Developer Days at GTC, which will showcase the many ways power users and developers can build extensions and apps on the platform. Hear from Omniverse engineering leaders and industry experts as they share new insights about 3D virtual world building, simulation, rendering, and more.

Additional resources 

Learn more by diving into the Omniverse Resource Center, which details how developers can build custom applications and extensions for the platform. 

For additional support, explore the Omniverse forums and Medium channel, tutorials on Twitter and YouTube, and join our Discord server to chat with the community.

Ultra rapid nanopore sequencing is bringing us one step closer to same-day whole genome genetic diagnosis.

Fast and cost-effective whole genome sequencing and analysis can be critical in a diagnostic setting. Recent advances in accelerated clinical sequencing, such as the world-record-setting DNA sequencing technique for rapid diagnosis, are bringing us one step closer to same-day, whole-genome genetic diagnosis.

A team led by Stanford University School of Medicine, NVIDIA, Google, UCSC and Oxford Nanopore Technologies (ONT) recently used this technique to identify disease-associated genetic variants that resulted in a diagnosis in just over 7 hours, with results published earlier this year in the New England Journal of Medicine.

This record-beating end-to-end genomic workflow is reliant on innovative technology and high-performance computation. Nanopore sequencing was implemented across 48 flow cells, with optimized methods enabling pore occupancy at 82%, rapidly generating 202 Gb in just a couple of hours. Analysis of the output was distributed across a Google Cloud computing environment, including basecalling and alignment across 16 instances of 4 x V100 GPUs (64 GPUs total), and variant calling across 14 instances of 4 x P100 GPUs (56 GPUs total).

Since the January NEJM publication, the NVIDIA Clara team has been optimizing the same whole genome workflow for the DGX-A100, giving clinicians and researchers the ability to deploy the same analysis as the world record approach on just eight A100 GPUs, and in just 4h10m for a 60x whole genome (Figure 1; benchmarked on the HG002 reference sample).

Not only does this enable fast analysis in a single server (8-GPU) framework, but it also lowers the cost per sample by two-thirds, from $568 to $183.

Basecalling and alignment

Basecalling is the process of classifying raw instrument signals into the bases A, C, G, and T of the genome. It is a computationally critical step in ensuring accuracy in all downstream analysis tasks. It is also an important data reduction step, reducing resultant data by approximately 10x.

At ~340 bytes per base, a single 30x coverage whole genome can easily be multiple terabytes in raw signals, as opposed to hundreds of gigabytes when processed. As such, it is beneficial for compute speed to rival sequencing output speed, which is non-trivial at a pace of ~450 bases per second through the 128,000 pores across 48 flow cells.

ONT’s PromethION P48 sequencer can generate as much as 10 terabases in a 72-hour run, equivalent to 96 human genomes (30x coverage).

The rapid classification task required for this already benefits from deep learning innovation and GPU acceleration. The core data processing toolkit for this purpose, Guppy, uses a recurrent neural network (RNN) for basecalling, with the option of two different architectures of either smaller (faster) or larger (higher accuracy) recurrent layer sizes.

The main computational bottleneck in basecalling is the RNN kernel, which has benefited from GPU integration with ONT sequencers, such as the desktop GridION Mk1 that includes a single V100 GPU and the handheld MinION Mk1C that includes a Jetson Edge platform.

Alignment is the process of taking the resultant basecalled fragments of DNA, now in the form of character strings of As, Cs, Gs, and Ts, and determining the genome location where those fragments originated, assembling a full genome from the massively parallelized sequencing process. This essentially rebuilds the full length genome from many 100-100,000bp long reads. For the world-record-setting sample, this totaled around 13million reads.

For the original world-record analysis, basecalling and alignment were run on separate instances of Guppy and Minimap2, respectively. In migrating this to a single-server DGX-A100 solution, and using Guppy’s integrated minimap2 aligner, you immediately save time on I/O. Through balancing of basecalling and alignment across the DGX eight A100 GPUs and 96 CPU threads, respectively, the two processes can be overlapped perfectly to align reads concurrently with basecalling, resulting in no impact on total runtime (

This brings the runtime of the basecalling and alignment step on the DGX-A100 to 2h 46m, which can also be overlapped with the sequencing itself. It is similar to the sequencing time expected for a 60x sample.

Variant calling

Variant calling is the portion of the workflow designed to identify all of the points in the newly assembled individual’s genome that differ from expected, compared to a reference genome. This involves scanning the full breadth of the genome to look for different types of variation. For example, this might include small single-base-pair variants all the way to large structural variants covering thousands of base-pairs. The world record pipeline used PEPPER-Margin-DeepVariant for small variants, and Sniffles for structural variants.

The PEPPER-Margin-DeepVariant approach is designed to optimize small variant calling for the long reads produced by nanopore sequencing.

• PEPPER identifies candidate variants through an RNN consisting of two bidirectional, gated, recurrent unit layers and a linear transformation layer.
• Margin then uses a hidden Markov model approach for a process called haplotyping, determining which variants have been inherited together from the maternal or paternal chromosomes. It passes this information to Google DeepVariant to use for maximum heterozygous variant calling accuracy.
• DeepVariant classifies final variants through a deep convolutional neural network, which is built on the Inception v2 architecture adapted specifically for DNA read pile-up input images.

Overall, PEPPER-Margin-DeepVariant allows the faster neural network of PEPPER to scan the whole genome for candidates, and then uses the larger neural network of DeepVariant for high accuracy variant calling of those candidates. To accelerate this pipeline, the world-record workflow used Parabricks DeepVariant, a GPU-accelerated implementation providing >20x faster runtimes than the open-source version on CPU (Figure 2).

The Clara team took this acceleration further by modifying PEPPER-Margin to run in an integrated fashion, splitting the data by chromosome and running the programs concurrently on GPU. PEPPER was also optimized for pipeline parameters such as batch sizes, number of workers, and number of callers, as well as upgrading PyTorch to enable support for NVIDIA Ampere Architecture acceleration of the RNN inference bottleneck.

For structural variant calling, Sniffles was upgraded to the recently released Sniffles 2, which is considerably more efficient, at 38x acceleration on CPU alone.

All these improvements put the runtime of the multiple variant calling stage at 1h 24m on the DGX-A100.

Powering real-time sequencing with NVIDIA DGX-A100

By bringing the world-record DNA sequencing technique for critical care patients to the DGX A100, the NVIDIA Clara team is powering real-time sequencing, simplifying a complex workflow on a single server, and cutting analysis costs by two-thirds. These improvements better enable long-read whole genome sequencing in a clinical care setting and help rare and undiagnosed disease patients get answers faster.

This pipeline will be available free for researchers. Request access today.

Featured image courtesy of Oxford Nanopore Technologies

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