Omics Domain Software Tools

Below are scientific software you may find useful for 'Omics analyses.

NVIDIA GPU Cloud (NGC)

• A resource which hosts containerized, GPU-accelerated scientific software.
• Site: https://catalog.ngc.nvidia.com/

Genome Sequencing

• Parabricks - GPU accelerated sequencing software:
  • Container on NGC service: https://catalog.ngc.nvidia.com/orgs/nvidia/collections/claraparabricks
  • See our Research Computing Parabricks Case Study

Single-Cell Transcriptomics

• RAPIDS-singlecell:
  • GPU accelerated clustering
  • blog: https://developer.nvidia.com/blog/gpu-accelerated-single-cell-rna-analysis-with-rapids-singlecell/
  • docs: https://rapids-singlecell.readthedocs.io/en/latest/
  • examples at ngc: https://catalog.ngc.nvidia.com/orgs/nvidia/teams/clara/containers/single-cell-examples_rapids
• Geneformer:
  • AI transformer model for SC transcriptomics
  • NGC: https://catalog.ngc.nvidia.com/orgs/nvidia/teams/clara/models/geneformer_100m

Spatial Genomics

• MONAI Vista:
  • Generalized GPU accelerated spatial genomics image segmentation
  • Vista2D:
    • NGC: https://catalog.ngc.nvidia.com/orgs/nvidia/teams/monaitoolkit/models/monai_vista2d
    • Blog: https://developer.nvidia.com/blog/advancing-cell-segmentation-and-morphology-analysis-with-nvidia-ai-foundation-model-vista-2d/
  • Vista3D:
    • NGC: https://catalog.ngc.nvidia.com/orgs/nvidia/teams/monaitoolkit/models/monai_vista3d