Individual skill
parabricks
Plan NVIDIA Parabricks pbrun commands, translate CPU options and check runtime readiness. Use for individual tools, including planning-only questions.
skills/bionemo-parabricks/SKILL.md
Source commit 25340619336e89bcc40365c28bfe9e790430468e
What was checked
- Matches the observed repository HEAD
- Yes
- Scanner rules are current
- Yes
- Repository scan complete
- No
- Skill scan complete
- No
- Observed behavior
- Network or broad shell
- Last checked
- Nov 2, 2026
These are observations at the recorded commit, not a guarantee of safety. Review the source before running it.
Install this skill
Choose an agent in your Stack or copy a command below. Commands fetch the pinned commit and copy only this skill directory. Existing destinations are refused. Copying a command does not install anything.
An install command is unavailable: current rules, complete repository and skill scans, an eligible behavior level and a permitted license are required.
Repository context
- Repository stars (not skill ratings)
- 3,882
- Repository last updated
- Nov 6, 2026
- License
- Apache-2.0
Observed agent integration: No specific integration evidence. Standard SKILL.md installation does not imply verified compatibility.
- agent-skills Repository topic
- agentic-ai Repository topic
- ai-agents Repository topic
- claude-code Repository topic
- codex Repository topic
- coding-agents Repository topic
- cuda Repository topic
- developer-tools Repository topic
- llm Repository topic
- omniverse Repository topic
- parabricks Declared skill tag
- genomics Declared skill tag
- nvidia Declared skill tag
- engineering Derived category
Files and excerpt
File metadata and permitted, redacted excerpts come from the recorded scan. Source links are pinned to that commit.
Browse files
BENCHMARK.mddoc · 13,871 bytesSKILL.mdcore · 11,331 bytesSKILL.mdcore · 11,331 bytesSKILL.mdcore · 11,331 bytesSKILL.mdcore · 11,331 bytesevals/evals.jsonasset · 63,426 bytesevals/files/rna-batch.jsonasset · 4,568 bytesevals/files/rna-contracts.jsonasset · 3,823 bytesreferences/command-conventions.mddoc · 7,042 bytesreferences/minimap2-controls.mddoc · 1,475 bytesreferences/pbrun-applybqsr.mddoc · 2,020 bytesreferences/pbrun-bam2fq.mddoc · 4,110 bytesreferences/pbrun-bammetrics.mddoc · 4,286 bytesreferences/pbrun-bamsort.mddoc · 2,629 bytesreferences/pbrun-bqsr.mddoc · 1,942 bytesreferences/pbrun-collectmultiplemetrics.mddoc · 5,463 bytesreferences/pbrun-dbsnp.mddoc · 1,788 bytesreferences/pbrun-deepsomatic.mddoc · 2,404 bytesreferences/pbrun-deepvariant.mddoc · 3,562 bytesreferences/pbrun-deepvariant_germline.mddoc · 2,674 bytesreferences/pbrun-fq2bam.mddoc · 6,530 bytesreferences/pbrun-fq2bam_meth.mddoc · 3,178 bytesreferences/pbrun-genotypegvcf.mddoc · 1,894 bytesreferences/pbrun-germline.mddoc · 3,020 bytesreferences/pbrun-giraffe.mddoc · 7,375 bytesreferences/pbrun-haplotypecaller.mddoc · 4,631 bytesreferences/pbrun-indexgvcf.mddoc · 2,928 bytesreferences/pbrun-markdup.mddoc · 4,190 bytesreferences/pbrun-minimap2.mddoc · 3,993 bytesreferences/pbrun-mutectcaller.mddoc · 3,395 bytesreferences/pbrun-ont_germline.mddoc · 2,419 bytesreferences/pbrun-pacbio_germline.mddoc · 2,499 bytesreferences/pbrun-pangenome_aware_deepvariant.mddoc · 5,783 bytesreferences/pbrun-pangenome_germline.mddoc · 3,973 bytesreferences/pbrun-postpon.mddoc · 1,143 bytesreferences/pbrun-prepon.mddoc · 1,400 bytesreferences/pbrun-rna_fq2bam.mddoc · 13,933 bytesreferences/pbrun-somatic.mddoc · 5,250 bytesreferences/pbrun-starfusion.mddoc · 9,733 bytesreferences/performance.mddoc · 1,868 bytesreferences/rna-translation.mddoc · 2,933 bytesreferences/runtime-environment.mddoc · 12,849 bytesreferences/shared-options.mddoc · 13,521 bytesreferences/tool-index.mddoc · 9,849 bytesscripts/check_parabricks_runtime.pyruns · 1,707 bytesscripts/check_parabricks_runtime.shruns · 26,441 bytesscripts/translate_star_to_parabricks.pyruns · 14,406 bytesskill-card.mddoc · 5,739 bytesskill.oms.sigasset · 14,625 bytes
Read excerpt
# Parabricks
## Purpose
Use this skill to discover the right NVIDIA Parabricks `pbrun` command, assess
runtime readiness, and generate version-aware command guidance for individual
tools.
Do **not** use this skill for whole-workflow inspection, acceleration planning,
or wiring optional GPU branches. For pipeline-level work, use
`genomics-workflow-acceleration`.
## When to Use This Skill