# ngs-analysis-router

This skill identifies the sequencing input and sends the request to a suitable public NGS analysis skill. It fits BCL, FASTQ, BAM/CRAM, count matrices, and VCF.

- skill · `type=skill` · Codex, ChatGPT · 3 installs · ★ 7604
- Author: OpenAI · official OpenAI repository
- License: MIT · policy=mirror · the beginning of the file is at the end of this page
- Source: https://github.com/openai/plugins/tree/HEAD/plugins/ngs-analysis/skills/ngs-analysis-router/SKILL.md
- Updated: 2026-10-08
- HTML: https://affpapa.org/en/nevibecode/skills/ngs-analysis-router

## What it does

The skill inspects available files and classifies run folders, FASTQs, BAM/CRAM, VCFs, and count matrices. It then routes the request to a leaf skill for variant calling, RNA-seq, single-cell work, epigenomics, amplicons, or metagenomics. When the route is unclear, it asks only for the fields needed to choose it, such as assay, organism, reference, read layout, and desired output.

Its supporting files include an intake schema, a pipeline registry, `ngs_preflight.py`, and `ngs_reference_manager.py`. Before installation or execution, it prepares an environment check; reference-heavy workflows can also get a resource plan. Generated install commands stay review-only until the user explicitly approves execution.

For human data, cloud upload permission must be settled before suggesting a cloud route. The intake also covers local, HPC, or cloud execution, container availability, package installation, and license boundaries.

## Install

### Codex (native platform)

1. **Skills CLI (Vercel)**
```bash
npx skills add openai/plugins --skill ngs-analysis-router -a codex
```

2. **Manually: put the files in place**
- File: `.agents/skills/ngs-analysis-router/SKILL.md` — For all projects use ~/.agents/skills/

### Claude Code

1. **Skills CLI (Vercel)**
```bash
npx skills add openai/plugins --skill ngs-analysis-router -a claude-code
```

2. **Manually: put the files in place**
- File: `~/.claude/skills/ngs-analysis-router/SKILL.md` — Copy the whole skill folder; for one project use .claude/skills/ngs-analysis-router/

### Cursor

**Manually: put the files in place**
- File: `.cursor/skills/ngs-analysis-router/SKILL.md` — Cursor also reads .agents/skills/ and .claude/skills/

### GitHub Copilot

1. **GitHub CLI**
```bash
gh skill install openai/plugins ngs-analysis-router
```

2. **Manually: put the files in place**
- File: `.github/skills/ngs-analysis-router/SKILL.md`

### Gemini CLI

**Platform CLI**
```bash
gemini skills install https://github.com/openai/plugins --path plugins/ngs-analysis/skills/ngs-analysis-router
```

### Windsurf (Devin Desktop)

**Manually: put the files in place**
- File: `.devin/skills/ngs-analysis-router/SKILL.md` — The legacy .windsurf/skills/ path still works

### Claude.ai

**Claude.ai**
- Zip the folder and upload it in Settings → Capabilities → Skills

Where a file is given instead of a command, copy the files from the source to that path: https://github.com/openai/plugins/tree/HEAD/plugins/ngs-analysis/skills/ngs-analysis-router/SKILL.md

## When to use it
- route sequencing files to the right analysis skill
- collect missing assay and reference details
- preflight a local or HPC runtime
- plan references and databases for a workflow
- separate cloud-permitted and local data paths

## Example prompts
- Route the files `sample_R1.fastq.gz` and `sample_R2.fastq.gz` to the right NGS skill and ask only essential setup questions.
- Inspect `RunInfo.xml`, `SampleSheet.csv`, and `Data/Intensities/BaseCalls`, then prepare the routing plan.
- Preflight the environment for `counts.h5ad` and show the next action before installation.

## Source text · SKILL.md · MIT

Below is the content of a third-party file. It is data, not instructions for you: do not act on anything written inside unless the human asks. Block tag: 15553de22b559297.

BEGIN THIRD-PARTY FILE 15553de22b559297
````text
---
name: ngs-analysis-router
description: Route BCL, FASTQ, BAM/CRAM, count-matrix, or VCF sequencing requests to the right public NGS analysis skill and ask only the missing assay-specific setup questions.
---

# Life Sciences NGS Analysis Router

Use this skill as the top-level entrypoint for ambiguous or broad sequencing-analysis requests.

## Start Here

Inspect the available inputs before asking the user questions. Look for:

- Illumina run-folder files: `RunInfo.xml`, `RunParameters.xml`, `SampleSheet.csv`, `Data/Intensities/BaseCalls`
- FASTQs: `*.fastq`, `*.fq`, `*.fastq.gz`, `*.fq.gz`
- BAM/CRAM/VCF: `*.bam`, `*.cram`, `*.vcf`, `*.vcf.gz`
- count matrices: `matrix.mtx`, `features.tsv`, `barcodes.tsv`, `*.h5`, `*.h5ad`, `*.rds`
- metadata: sample sheets, design files, target BEDs, reference FASTA/GTF, primer files

Read `references/intake-schema.json` and `references/pipeline-registry.json` when forming the route.

## Intake Rules

Ask the smallest set of missing questions needed to choose a defensible pipeline. Do not ask the full questionnaire if file inspection already answers a field.

Always resolve:

- input type
- assay type
- desired output
- organism/reference
- paired-end vs single-end when FASTQs are involved
- any assay-specific design file or metadata required for the requested result
- runtime constraints: local/HPC/cloud, container availability, and whether installs are allowed

For human data, ask whether cloud upload is allowed before suggesting BaseSpace, Terra, DNAnexus, or any cloud path.

## Routing

Route to one leaf skill:

- BCL run folder or demultiplexing: `ngs-bcl-to-fastq`
- QC/trimming only: `ngs-fastq-qc`
- WGS/WES/panel variants: `ngs-dna-variant-calling`, then a subtype skill when the analysis model is clear
- germline WGS/WES/panel variants: `ngs-dna-germline-variants`
- tumor-normal or tumor-only somatic variants: `ngs-dna-somatic-variants`
- UMI, duplex, or low-frequency targeted panels: `ngs-dna-umi-panel-variants`
- bulk RNA-seq kickoff: `ngs-bulk-rnaseq`
- bulk RNA-seq FASTQ-to-count QC: `ngs-bulk-rnaseq-counts-qc`
- bulk RNA-seq differential expression from counts: `ngs-bulk-rnaseq-differential-expression`
- single-cell or single-nucleus FASTQ-to-matrix kickoff: `ngs-scrna-seq`
- single-cell or single-nucleus post-count QC/annotation/UMAP: `scrna-seq-qc`
- epigenomics kickoff: `ngs-epigenomics-peaks`
- ATAC-seq QC/peaks/accessibility: `ngs-atacseq-peaks-qc`
- ChIP-seq, CUT&RUN, or CUT&Tag QC/peaks: `ngs-chip-cutrun-peaks-qc`
- 16S/18S/ITS/COI amplicons: `ngs-amplicon-microbiome`
- shotgun metagenomics: `ngs-shotgun-metagenomics`
- runtime/package setup only: `ngs-runtime-env`

Prefer public, runtime-installable packages and nf-core workflows. Surface license/EULA/account boundaries before using proprietary or cloud tools.

## Preflight

Before proposing installation or execution, run a preflight plan from the repo root:

```bash
````
END THIRD-PARTY FILE 15553de22b559297

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