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GPU-native genomics
Docs · OGN platform

GPU-native genomics operating system

From raw reads to GIAB-validated variant calls in a continuous GPU pipeline. This is the control surface for the engine: CLI, pipelines, benchmarks, and deployment runbooks.

CUDA 12+Hopper · AmpereGIAB-validated flowsSchemas stable
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OGN Core Kit (open source)
Benchmark packExample pipelinesGitHub

OGN Core Kit (open adoption surface)

OGN Core Kit is the public integration surface for Omnis Genome Nexus (OGN): the stable contracts, the worker runner, SDKs, and workflow adapters. It does not include the proprietary OGN engine binaries or GPU kernels.
GitHub: https://github.com/omniscoder/ogn-core-kit

What you get

  • Job Spec JSON v1 (docs + JSON schema + conformance fixtures)
  • ogn-runner: stable worker entrypoint (ogn-runner -) that executes an engine and uploads artifacts
  • Python package ogn-sdk: ogn CLI + ogn_sdk helpers + ogn_runner
  • Workflow adapters (example Nextflow pipeline)

Install (Python)

BashPowerShellPython API (coming)
ogn CLI
python -m pip install ogn-sdk
ogn-runner --help

Engine requirement

To run real genomics compute you need access to an OGN engine binary or container image (distributed separately).
ogn-runner shells out to an engine executable (defaults to ogn_run on PATH):
BashPowerShellPython API (coming)
ogn CLI
export OGN_ENGINE_BIN=/path/to/ogn_run

Using ogn-runner

Workers are expected to run:
BashPowerShellPython API (coming)
ogn CLI
ogn-runner -
where the Job Spec JSON v1 payload is provided on stdin.
For local testing you can also pass a file path:
BashPowerShellPython API (coming)
ogn CLI
ogn-runner job_spec.json
Upload behavior:
  • If outputs.*.put_url is present, the runner uploads via presigned HTTP PUT.
  • If put_url is absent, the runner uploads directly to the stable outputs.*.uri when supported (e.g. s3://...).

Contracts

The canonical contract lives in the core kit repo:
  • spec/v1/jobspec.md
  • spec/v1/jobspec.schema.json
  • spec/v1/conformance/
Job Spec v1 is additive-only and consumers must ignore unknown fields.
OGN Core Kit (open source) | OGN documentation | Omnis Genomics