Agent skill

Parabricks

by NVIDIA-BioNeMo in NVIDIA-BioNeMo/bionemo-agent-toolkit

Route NVIDIA Parabricks pbrun tools, assess GPU/runtime readiness, and provide version-aware command guidance for FASTQ/BAM processing, RNA-seq, variant calling, BAM QC, and GVCF workflows.

Apache-2.0Auto-check passedResearch & Science

Install Parabricks

skills CLI

$ npx skills add NVIDIA-BioNeMo/bionemo-agent-toolkit --skill parabricks -a claude-code

Project install by default; add -g for ~/.claude/skills/.

GitHub CLI

$ gh skill install NVIDIA-BioNeMo/bionemo-agent-toolkit parabricks --agent claude-code

Project scope by default; add --scope user for a personal install. Needs GitHub CLI 2.90.0 or later (public preview).

Manual copy

$ git clone --depth 1 https://github.com/NVIDIA-BioNeMo/bionemo-agent-toolkit.git skills-src && mkdir -p .claude/skills && cp -r skills-src/library-skills/parabricks .claude/skills/parabricks && rm -rf skills-src

Use ~/.claude/skills/ instead of .claude/skills for a personal install. The folder must contain SKILL.md.

Claude Code skills documentation · loads skills from .claude/skills/

Paste into Claude Code

Install the "parabricks" agent skill from https://github.com/NVIDIA-BioNeMo/bionemo-agent-toolkit/tree/main/library-skills/parabricks into .claude/skills/parabricks/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "parabricks", then confirm the skill loads.

Claude Code copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.

$skill-installer

$skill-installer install https://github.com/NVIDIA-BioNeMo/bionemo-agent-toolkit/tree/main/library-skills/parabricks

Type this inside Codex. $skill-installer <name> installs a curated skill from openai/skills. The installer writes to $CODEX_HOME/skills (default ~/.codex/skills). Restart Codex if the skill does not show up.

skills CLI

$ npx skills add NVIDIA-BioNeMo/bionemo-agent-toolkit --skill parabricks -a codex

Project install goes to .agents/skills/; add -g for ~/.codex/skills/.

GitHub CLI

$ gh skill install NVIDIA-BioNeMo/bionemo-agent-toolkit parabricks --agent codex

Project scope by default (.agents/skills/); add --scope user for a personal install.

Manual copy

$ git clone --depth 1 https://github.com/NVIDIA-BioNeMo/bionemo-agent-toolkit.git skills-src && mkdir -p .agents/skills && cp -r skills-src/library-skills/parabricks .agents/skills/parabricks && rm -rf skills-src

Use ~/.agents/skills/ instead of .agents/skills for a personal install.

Codex skills documentation · loads skills from .agents/skills/

Paste into Codex

Install the "parabricks" agent skill from https://github.com/NVIDIA-BioNeMo/bionemo-agent-toolkit/tree/main/library-skills/parabricks into .agents/skills/parabricks/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "parabricks", then confirm the skill loads.

Codex copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.

skills CLI

$ npx skills add NVIDIA-BioNeMo/bionemo-agent-toolkit --skill parabricks -a cursor

Project install goes to .agents/skills/; add -g for ~/.cursor/skills/.

GitHub CLI

$ gh skill install NVIDIA-BioNeMo/bionemo-agent-toolkit parabricks --agent cursor

Project scope by default (.agents/skills/); add --scope user for a personal install.

Manual copy

$ git clone --depth 1 https://github.com/NVIDIA-BioNeMo/bionemo-agent-toolkit.git skills-src && mkdir -p .cursor/skills && cp -r skills-src/library-skills/parabricks .cursor/skills/parabricks && rm -rf skills-src

Use ~/.cursor/skills/ instead of .cursor/skills for a personal install.

Cursor skills documentation · loads skills from .cursor/skills/, .agents/skills/, .claude/skills/, .codex/skills/

Paste into Cursor

Install the "parabricks" agent skill from https://github.com/NVIDIA-BioNeMo/bionemo-agent-toolkit/tree/main/library-skills/parabricks into .cursor/skills/parabricks/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "parabricks", then confirm the skill loads.

Cursor copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.

gemini skills install

$ gemini skills install https://github.com/NVIDIA-BioNeMo/bionemo-agent-toolkit.git --path library-skills/parabricks

--scope user (default) or --scope workspace; --path is the subfolder of the repo that holds the skill; --consent skips the security confirmation prompt.

skills CLI

$ npx skills add NVIDIA-BioNeMo/bionemo-agent-toolkit --skill parabricks -a gemini-cli

Project install goes to .agents/skills/; add -g for ~/.gemini/skills/.

GitHub CLI

$ gh skill install NVIDIA-BioNeMo/bionemo-agent-toolkit parabricks --agent gemini-cli

Project scope by default (.agents/skills/); add --scope user for a personal install.

Manual copy

$ git clone --depth 1 https://github.com/NVIDIA-BioNeMo/bionemo-agent-toolkit.git skills-src && mkdir -p .gemini/skills && cp -r skills-src/library-skills/parabricks .gemini/skills/parabricks && rm -rf skills-src

Use ~/.gemini/skills/ instead of .gemini/skills for a personal install, then run /skills reload.

Gemini CLI skills documentation · loads skills from .gemini/skills/, .agents/skills/

Paste into Gemini CLI

Install the "parabricks" agent skill from https://github.com/NVIDIA-BioNeMo/bionemo-agent-toolkit/tree/main/library-skills/parabricks into .gemini/skills/parabricks/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "parabricks", then confirm the skill loads.

Gemini CLI copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.

GitHub CLI

$ gh skill install NVIDIA-BioNeMo/bionemo-agent-toolkit parabricks

Installs for Copilot at project scope by default; add --scope user for a personal install. Preview a skill first with gh skill preview. Needs GitHub CLI 2.90.0 or later (public preview).

skills CLI

$ npx skills add NVIDIA-BioNeMo/bionemo-agent-toolkit --skill parabricks -a github-copilot

Project install goes to .agents/skills/; add -g for ~/.copilot/skills/.

Manual copy

$ git clone --depth 1 https://github.com/NVIDIA-BioNeMo/bionemo-agent-toolkit.git skills-src && mkdir -p .github/skills && cp -r skills-src/library-skills/parabricks .github/skills/parabricks && rm -rf skills-src

Use ~/.copilot/skills/ instead of .github/skills for a personal install. Commit .github/skills so cloud agent and code review can use it.

GitHub Copilot skills documentation · loads skills from .github/skills/, .claude/skills/, .agents/skills/

Paste into GitHub Copilot

Install the "parabricks" agent skill from https://github.com/NVIDIA-BioNeMo/bionemo-agent-toolkit/tree/main/library-skills/parabricks into .github/skills/parabricks/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "parabricks", then confirm the skill loads.

GitHub Copilot copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.

skills CLI

$ npx skills add NVIDIA-BioNeMo/bionemo-agent-toolkit --skill parabricks -a opencode

OpenCode documents no install command of its own. Project install goes to .agents/skills/; add -g for ~/.config/opencode/skills/.

GitHub CLI

$ gh skill install NVIDIA-BioNeMo/bionemo-agent-toolkit parabricks --agent opencode

Project scope by default (.agents/skills/); add --scope user for a personal install.

Manual copy

$ git clone --depth 1 https://github.com/NVIDIA-BioNeMo/bionemo-agent-toolkit.git skills-src && mkdir -p .opencode/skills && cp -r skills-src/library-skills/parabricks .opencode/skills/parabricks && rm -rf skills-src

Use ~/.config/opencode/skills/ instead of .opencode/skills for a personal install.

OpenCode skills documentation · loads skills from .opencode/skills/, .claude/skills/, .agents/skills/

Paste into OpenCode

Install the "parabricks" agent skill from https://github.com/NVIDIA-BioNeMo/bionemo-agent-toolkit/tree/main/library-skills/parabricks into .opencode/skills/parabricks/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "parabricks", then confirm the skill loads.

OpenCode copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.

Facts

Skill name: parabricks
GitHub stars: 478
Token cost: ~2.1k tokens
SKILL.md length: 657 words
Files: 38 (incl. scripts, references)
Skills in repo: 14
Repo updated: Oct 6, 2026
First seen: Oct 7, 2026
Licence: Apache-2.0

At a glance

Route NVIDIA Parabricks pbrun tools, assess GPU/runtime readiness, and provide version-aware command guidance for FASTQ/BAM processing, RNA-seq, variant calling, BAM QC, and GVCF workflows.

Works in 4 steps: Confirm the Parabricks version or… → Classify the request → Collect missing biological and… → …
Accelerating whole pipelines — use genomics-workflow-acceleration
SKILL.md covers Purpose, When to Use This Skill, Prerequisites and Limitations, plus 7 more sections
Calls python3 and docker

What it does

Parabricks is an agent skill from NVIDIA-BioNeMo/bionemo-agent-toolkit. Route NVIDIA Parabricks pbrun tools, assess GPU/runtime readiness, and provide version-aware command guidance for FASTQ/BAM processing, RNA-seq, variant calling, BAM QC, and GVCF workflows. Do NOT use for inspecting or accelerating whole pipelines — use genomics-workflow-acceleration.

Its SKILL.md is about 2.1k tokens, which your agent loads only when the skill is triggered. The skill folder holds 39 other files, including scripts and reference files (for example `.skillsource.json`, `evals/evals.json` and `references/parabricks-rna-validate.md`).

It sits in Research & Science, covering Bioinformatics. It works with NVIDIA AI Platform. The repository describes itself as: Turn any agent into a life science expert with NVIDIA BioNeMo skills. The licence is Apache-2.0.

When your agent uses it

Accelerating whole pipelines — use genomics-workflow-acceleration
Tasks that involve Bioinformatics

Example prompts

“/parabricks”

Requirements

Python 3
Docker

Workflow steps

4 steps, taken from the first numbered list in SKILL.md.

Confirm the Parabricks version or container tag. Verify the current NVIDIA
Classify the request
Collect missing biological and filesystem context before generating commands.
Generate conservative Docker commands with explicit mounts, workdir, and

What it can do on your machine

Read from SKILL.md and the folder at commit 2113472. It shows what the files ask for, not the result of running them.

Tool permissions
Pre-approves nothing: there is no allowed-tools line, so your agent's usual permission prompts apply.
From allowed-tools in the SKILL.md frontmatter.
Runs code
Ships 1 file in scripts/, which the agent can run.
Shell commands in SKILL.md call:
- python3
- docker
From the folder's file list and the shell code blocks in SKILL.md.
Network
Links to these hosts (documentation or services it may open):
- docs.nvidia.com
From URLs in SKILL.md, links to its own repository left out.
Credentials
Names no API keys, tokens, secrets or passwords.
From names ending in _API_KEY, _TOKEN, _SECRET, _KEY or _PASSWORD in SKILL.md.

Context cost

Parabricks loads about 2.1k tokens when it runs, and up to ~46k if it reads all its reference files. Until then it costs about 74 tokens; SKILL.md has 657 words of instructions outside code blocks.

Always · name and description, kept in context so the agent knows when to use it: ~74
When it runs · the whole SKILL.md, loaded when a task matches: ~2.1k
With references · SKILL.md plus every file in references/, read only if the agent opens them: ~46k

Estimates: characters ÷ 4, the usual rule of thumb; real counts depend on the model's tokenizer. Scripts and assets cost tokens only if the agent reads them.

Safety

Auto-check passed

The automated check found no risky patterns in SKILL.md.

Automated static check — not a guarantee. Review scripts before installing. It scans the text of SKILL.md for risky patterns (piping downloads into a shell, reading credential files, hidden Unicode, destructive commands); the scripts in this folder are not scanned.

SKILL.md

The full file from NVIDIA-BioNeMo/bionemo-agent-toolkit at commit 2113472, republished under its Apache-2.0 licence (© NVIDIA-BioNeMo). 657 words, ~2,093 tokens.

Download SKILL.mdSave it as .claude/skills/parabricks/SKILL.md (or your agent's skills folder). This skill also uses 37 other files; get the full folder from GitHub.

name: parabricks
description: Route NVIDIA Parabricks pbrun tools, assess GPU/runtime readiness, and provide version-aware command guidance for FASTQ/BAM processing, RNA-seq, variant calling, BAM QC, and GVCF workflows. Do NOT use for inspecting or accelerating whole pipelines — use genomics-workflow-acceleration.
license: CC-BY-4.0 AND Apache-2.0
metadata.version: 1.1.0
metadata.tags: parabricks, genomics, nvidia

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 and pipelines.

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

Which pbrun tool fits the user's data and goal
GPU, driver, Docker, container, storage, or installation readiness
Command shape, flags, and validation for a specific Parabricks tool
Troubleshooting a single Parabricks command or tool family

Prerequisites

Ask for input data type, sequencing technology, reference build, sample structure, desired output, target Parabricks version/container tag, and runtime target before recommending commands.

If the user is unsure which tool applies, read tool-index.md first, then load the matching references/pbrun-<tool>.md file.

Limitations

This skill routes and guides Parabricks commands. It does not install Parabricks, infer missing sample metadata, guarantee output parity, provide clinical interpretation, or promise exact runtime without benchmark data.

Workflow

Confirm the Parabricks version or container tag. Verify the current NVIDIA docs when the user asks for the latest tool list or version-sensitive flags.
Classify the request:
- Runtime → runtime-environment.md
- Tool discovery → tool-index.md
- Specific command → matching references/pbrun-<tool>.md
Collect missing biological and filesystem context before generating commands.
Generate conservative Docker commands with explicit mounts, workdir, and placeholders. Validate paths, indexes, and outputs after command generation.

Tool Reference Index

Load only the reference file for the selected tool.

Tool	Reference	Use when
`applybqsr`	pbrun-applybqsr.md	Apply BQSR table to aligned BAM
`bam2fq`	pbrun-bam2fq.md	BAM → FASTQ conversion
`bamsort`	pbrun-bamsort.md	Standalone BAM sort
`bqsr`	pbrun-bqsr.md	Generate BQSR recalibration table
`fq2bam`	pbrun-fq2bam.md	Short-read DNA paired FASTQ → BAM/CRAM
`fq2bam_meth`	pbrun-fq2bam_meth.md	Bisulfite/methylation FASTQ → BAM/CRAM
`giraffe`	pbrun-giraffe.md	Pangenome graph alignment
`markdup`	pbrun-markdup.md	Standalone duplicate marking
`minimap2`	pbrun-minimap2.md	Long-read FASTQ alignment
`rna_fq2bam`	pbrun-rna_fq2bam.md	RNA-seq FASTQ(s) → splice-aware BAM (STAR alignment)
`starfusion`	pbrun-starfusion.md	Fusion detection from chimeric junction input + STAR-Fusion genome library
`germline`	pbrun-germline.md	GATK-style germline pipeline from FASTQ
`deepvariant_germline`	pbrun-deepvariant_germline.md	DeepVariant germline pipeline from FASTQ
`haplotypecaller`	pbrun-haplotypecaller.md	Standalone HaplotypeCaller from BAM/CRAM
`deepvariant`	pbrun-deepvariant.md	Standalone DeepVariant from BAM/CRAM
`somatic`	pbrun-somatic.md	Tumor-normal somatic pipeline
`mutectcaller`	pbrun-mutectcaller.md	Mutect2-compatible somatic calling
`deepsomatic`	pbrun-deepsomatic.md	DeepSomatic-based somatic calling
`pacbio_germline`	pbrun-pacbio_germline.md	PacBio long-read germline
`ont_germline`	pbrun-ont_germline.md	Oxford Nanopore long-read germline
`pangenome_germline`	pbrun-pangenome_germline.md	Pangenome-aware germline
`pangenome_aware_deepvariant`	pbrun-pangenome_aware_deepvariant.md	Pangenome-aware DeepVariant
`prepon`	pbrun-prepon.md	Pangenome-aware preprocessing
`postpon`	pbrun-postpon.md	Pangenome-aware post-processing
`bammetrics`	pbrun-bammetrics.md	Whole-genome coverage/depth metrics
`collectmultiplemetrics`	pbrun-collectmultiplemetrics.md	Multiple Picard/GATK-style alignment metrics
`genotypegvcf`	pbrun-genotypegvcf.md	Joint-genotype GVCF input(s) into VCF
`indexgvcf`	pbrun-indexgvcf.md	Index GVCF input
`dbsnp`	pbrun-dbsnp.md	dbSNP annotation on variant files

For routing heuristics when multiple tools could apply, see tool-index.md.

Show full SKILL.md (238 more words)Show less

Runtime Readiness

For GPU, driver, Docker, container, storage, or installation questions, read runtime-environment.md and prefer:

bash

python3 skills/parabricks/scripts/check_parabricks_runtime.py

Add --path <dir> for known input/output/tmp paths. Run container probes only with user consent.

Command Shape

bash

docker run --rm --gpus all \
  --volume /host/input:/workdir \
  --volume /host/output:/outputdir \
  --workdir /workdir \
  nvcr.io/nvidia/clara/clara-parabricks:<version> \
  pbrun <selected-tool> \
  <tool-specific-options>

Check the version-specific tool reference before finalizing flags.

Troubleshooting

Error	Cause	Solution
Multiple plausible tools	Data type or goal underspecified	Ask for assay, inputs, caller preference, desired output; use tool-index
Exact flag requested	Options are version-sensitive	Check the selected tool reference and NVIDIA docs
Runtime question	GPU, Docker, drivers, or storage	Use runtime-environment reference and diagnostic script
Wrong tool family	Assay or input type unclear	Confirm DNA/RNA/methylation/long-read/pangenome before routing
CUDA or memory failure	Runtime not ready or GPU memory constrained	Assess runtime before tuning command flags

Guardrails

Treat command availability and options as version-sensitive.
Do not infer exact flags from command names alone.
Do not collapse standalone tools and full pipelines when explaining tradeoffs.
Do not substitute DNA fq2bam for RNA, or germline for somatic callers.
Do not invent sample names, read groups, reference builds, known-sites files, model files, graph resources, container tags, or output paths.
Do not install, upgrade, or modify packages. Label setup commands as user-run.
Do not claim CPU execution of Parabricks tools.
Do not claim biological or VCF parity without a comparison run.
Prefer official NVIDIA docs for exact command syntax and option defaults.

Key References

Parabricks tool index: https://docs.nvidia.com/clara/parabricks/latest/toolreference.html
Output accuracy and compatible CPU software versions: https://docs.nvidia.com/clara/parabricks/latest/documentation/tooldocs/outputaccuracyandcompatiblecpusoftwareversions.html
Getting started: https://docs.nvidia.com/clara/parabricks/latest/gettingstarted.html
Overview: https://docs.nvidia.com/clara/parabricks/latest/overview.html

Files

SKILL.md and 37 other files (scripts, references) in library-skills/parabricks of NVIDIA-BioNeMo/bionemo-agent-toolkit.

SKILL.md
.skillsource.json
evals/evals.json
references/parabricks-rna-validate.md
references/pbrun-applybqsr.md
references/pbrun-bam2fq.md
references/pbrun-bammetrics.md
references/pbrun-bamsort.md
references/pbrun-bqsr.md
references/pbrun-collectmultiplemetrics.md
references/pbrun-dbsnp.md
references/pbrun-deepsomatic.md
references/pbrun-deepvariant.md
references/pbrun-deepvariant_germline.md
references/pbrun-fq2bam.md
references/pbrun-fq2bam_meth.md
references/pbrun-genotypegvcf.md
references/pbrun-germline.md
references/pbrun-giraffe.md
… and 19 more

Open the folder on GitHubat commit 2113472

Compare with similar skills

Parabricks next to the 5 skills that share the most tags, products or categories with it. Stars are the repository's; “used in” counts other GitHub owners with a copy.

Parabricks compared with similar skills
Skill	Stars	Used in	Tokens	Auto-check	Licence	Repo updated
Parabricks this skillNVIDIA-BioNeMo/bionemo-agent-toolkit	478	—	~2.1k	Automated safety check: Pass	Apache-2.0	yesterday
Evo2 NimNVIDIA/skills	3.5k	1 repos	~2.4k	Automated safety check: Notes	Apache-2.0	yesterday
Alphagenome Single Variant Analysisgoogle-deepmind/science-skills	3.2k	2 repos	~3k	Automated safety check: Notes	Apache-2.0	22 days ago
13C Metabolic Flux AnalysisK-Dense-AI/scientific-agent-skills	48k	1 repos	~3.2k	Automated safety check: Pass	MIT	2 days ago
Clinvar Databasegoogle-deepmind/science-skills	3.2k	2 repos	~3.9k	Automated safety check: Notes	Apache-2.0	22 days ago
Metabolic Study Planneraiming-lab/AutoResearchClaw	15k	—	~1.9k	Automated safety check: Pass	MIT	1 mo ago

Similar skills

Evo2 Nim
NVIDIA/skills
Official
Generate and analyze DNA sequences using NVIDIA's Evo 2 BioNeMo NIM microservice.
3.5k GitHub starsUsed in 1 repo~2.4k tokens
DevOps & CloudAuto-check: notes
Alphagenome Single Variant Analysis
google-deepmind/science-skills
Analyzes genetic variant effects on gene expression (RNA-seq), chromatin accessibility (DNASE), histone marks (ChIP), and transcription factors using the AlphaGenome API.
3.2k GitHub starsUsed in 2 repos~3k tokens
Research & ScienceAuto-check: notes
13C Metabolic Flux Analysis
K-Dense-AI/scientific-agent-skills
Estimates reaction fluxes inside cells from steady-state carbon-13 labeling data with a bundled mfapy-based solver, and reports which fluxes the data pin down.
48k GitHub starsUsed in 1 repo~3.2k tokens
Research & ScienceAuto-check passed
Clinvar Database
google-deepmind/science-skills
A skill your agent uses when needing clinical significance, pathogenicity classifications (e.g., Pathogenic, Benign, VUS), clinical evidence rationales, or finding "hard positive" benchmark controls…
3.2k GitHub starsUsed in 2 repos~3.9k tokens
Research & ScienceAuto-check: notes
Metabolic Study Planner
aiming-lab/AutoResearchClaw
Turns a broad metabolic modelling topic into a concrete, paper-shaped plan with organism, model, perturbations, metrics and figures before any FBA code is written.
15k GitHub stars~1.9k tokensUpdated 1 mo ago
Research & ScienceAuto-check passed
Dbsnp Database
google-deepmind/science-skills
A skill your agent uses when you want to look up, map, and search for short genetic variants (SNPs, indels) in NCBI's dbSNP database.
3.2k GitHub starsUsed in 2 repos~3.4k tokens
Research & ScienceAuto-check: notes

More from NVIDIA-BioNeMo/bionemo-agent-toolkit

All 14 skills in this repo

Complexa Binder Design
NVIDIA-BioNeMo/bionemo-agent-toolkit
Run a complete protein binder design campaign with NVIDIA Proteina-Complexa: resolve a target structure and hotspots from a name/sequence/PDB, co-design binder sequence+structure with reward-guided…
478 GitHub stars~3.1k tokensUpdated yesterday
Auto-check: notes
Protein Binder Design
NVIDIA-BioNeMo/bionemo-agent-toolkit
Orchestrate an end-to-end de novo protein binder design campaign against a protein target by composing BioNeMo NIM skills.
478 GitHub stars~1.4k tokensUpdated yesterday
Auto-check: notes
Cuequivariance
NVIDIA-BioNeMo/bionemo-agent-toolkit
Build and debug cuEquivariance irreps, custom Irrep subclasses, Clebsch-Gordan tensor products, and equivariant or segmented polynomials.
478 GitHub stars~1.9k tokensUpdated yesterday
Auto-check passed
Genomics Workflow Acceleration
NVIDIA-BioNeMo/bionemo-agent-toolkit
A skill your agent uses when accelerating existing genomics workflows with NVIDIA Parabricks, improving runtime or price/performance, converting pipeline steps to GPUs, or comparing CPU and GPU…
478 GitHub stars~3.3k tokensUpdated yesterday
Auto-check passed
Complexa Design
NVIDIA-BioNeMo/bionemo-agent-toolkit
End-to-end Proteina-Complexa design pipeline driver. An agent skill from NVIDIA-BioNeMo/bionemo-agent-toolkit.
478 GitHub stars~4.1k tokensUpdated yesterday
Auto-check: notes
Complexa Evaluate Pdbs
NVIDIA-BioNeMo/bionemo-agent-toolkit
Standalone evaluation of an existing PDB directory with Proteina-Complexa.
478 GitHub stars~3.3k tokensUpdated yesterday
Auto-check: notes

Works with

NVIDIA AI Platform

Questions about Parabricks

What does Parabricks do?

Route NVIDIA Parabricks pbrun tools, assess GPU/runtime readiness, and provide version-aware command guidance for FASTQ/BAM processing, RNA-seq, variant calling, BAM QC, and GVCF workflows. Parabricks is an agent skill from NVIDIA-BioNeMo/bionemo-agent-toolkit. Route NVIDIA Parabricks pbrun tools, assess GPU/runtime readiness, and provide version-aware command guidance for FASTQ/BAM processing, RNA-seq, variant calling, BAM QC, and GVCF workflows.

When should I use Parabricks?

Parabricks fits situations like: accelerating whole pipelines — use genomics-workflow-acceleration; tasks that involve Bioinformatics.

How do I install Parabricks in Claude Code?

Run `npx skills add NVIDIA-BioNeMo/bionemo-agent-toolkit --skill parabricks -a claude-code`. Or copy the skill folder (library-skills/parabricks in NVIDIA-BioNeMo/bionemo-agent-toolkit) into .claude/skills/parabricks in your project. Claude Code loads it when a task matches its description.

How do I install Parabricks in Codex?

Run `npx skills add NVIDIA-BioNeMo/bionemo-agent-toolkit --skill parabricks -a codex`. Or copy the skill folder (library-skills/parabricks in NVIDIA-BioNeMo/bionemo-agent-toolkit) into .agents/skills/parabricks in your project. Codex loads it when a task matches its description.

Can I use Parabricks in Cursor, Gemini CLI or GitHub Copilot?

Cursor, Gemini CLI, GitHub Copilot and OpenCode also load SKILL.md folders. With the skills CLI, run `npx skills add NVIDIA-BioNeMo/bionemo-agent-toolkit --skill parabricks -a cursor` (or -a gemini-cli, github-copilot or opencode for the others). To copy it by hand, put the folder in .cursor/skills/parabricks, .gemini/skills/parabricks, .github/skills/parabricks and .opencode/skills/parabricks in your project.

What does Parabricks need to run?

Going by SKILL.md and its folder, Parabricks needs the command-line tools its instructions call (python3 and docker). Our summary lists: Python 3; Docker.

Does Parabricks access the network?

SKILL.md names 1 domain. As links in the text: docs.nvidia.com. This is read from the text; nothing was executed.

Is Parabricks safe to install?

Our automated static check of SKILL.md found no risky patterns, such as piping downloads into a shell, reading credential files or hidden Unicode. It is not a guarantee. The check reads SKILL.md only: the scripts in the folder are not scanned, so read them before running anything.

What licence does Parabricks use?

Parabricks is published under the Apache-2.0 licence (declared in SKILL.md). It allows redistribution, so the full SKILL.md is shown on this page.

How many tokens does Parabricks use?

About 2.1k tokens (SKILL.md is roughly 8.4k characters). Agents keep only the skill's name and description in context until a task matches; then they load SKILL.md in full. Its references folder adds about 44k tokens, read only when the agent opens those files.

What are the alternatives to Parabricks?

Skills that share tags, products or a category with Parabricks: Evo2 Nim (NVIDIA/skills, 3.5k stars), Alphagenome Single Variant Analysis (google-deepmind/science-skills, 3.2k stars), 13C Metabolic Flux Analysis (K-Dense-AI/scientific-agent-skills, 48k stars) and Clinvar Database (google-deepmind/science-skills, 3.2k stars). The comparison table on this page puts their stars, adoption, token cost, safety result and licence side by side.

Who maintains Parabricks?

NVIDIA-BioNeMo (a GitHub organization) maintains it in NVIDIA-BioNeMo/bionemo-agent-toolkit, which has 478 GitHub stars. The repository holds 14 skills in this directory. The repository was last updated on October 6, 2026.

Source: NVIDIA-BioNeMo/bionemo-agent-toolkit on GitHub. Facts on this page come from the repository at the commit we read; the author's words are quoted as theirs.

Install Parabricks

Facts

At a glance

What it does

When your agent uses it

Example prompts

Requirements

Workflow steps

What it can do on your machine

Tool permissions

Runs code

Network

Credentials

Context cost

Safety

SKILL.md

Parabricks

Purpose

When to Use This Skill

Prerequisites

Limitations

Workflow

Tool Reference Index

Runtime Readiness

Command Shape

Troubleshooting

Guardrails

Key References

Files

Compare with similar skills

Similar skills

More from NVIDIA-BioNeMo/bionemo-agent-toolkit

Related

Questions about Parabricks