# ngs-bcl-to-fastq

Validates an Illumina run folder and sample sheet, plans demultiplexing, and runs BCL-to-FASTQ conversion. Useful when the input is a sequencing run folder.

- skill · `type=skill` · Codex, ChatGPT · 2 installs · ★ 7596
- 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-bcl-to-fastq/SKILL.md
- Updated: 2026-10-08
- HTML: https://affpapa.org/en/nevibecode/skills/ngs-bcl-to-fastq

## What it does

The skill handles the whole demultiplexing prep, not just a command wrapper. It first checks the structure: whether `RunInfo.xml`, `SampleSheet.csv`, and the `BaseCalls` directory exist. Then it compares index lengths against index reads, looks for duplicate sample/index combinations within each lane, and pins down i5 orientation for dual-index runs and UMI layout.

Conversion runs through the plugin-owned runner `plugins/ngs-analysis/scripts/run_bcl_to_fastq.py`. It takes the run folder path, the sample sheet, and an output directory. Conversion starts only with the `--execute` flag. If neither `bcl-convert` nor `bcl2fastq` is installed, the runner records the blocker instead of downloading proprietary software on its own.

\`bcl-convert` is free for local use but RPM-distributed by Illumina, so the skill will not auto-download it. That is a reason to confirm the tool is already present before you kick off conversion. After conversion the skill reviews metrics: total clusters, clusters passing filter, percent assigned and percent undetermined by lane, and per-sample read counts.

## Install

### Codex (native platform)

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

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

### Claude Code

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

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

### Cursor

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

### GitHub Copilot

1. **GitHub CLI**
```bash
gh skill install openai/plugins ngs-bcl-to-fastq
```

2. **Manually: put the files in place**
- File: `.github/skills/ngs-bcl-to-fastq/SKILL.md`

### Gemini CLI

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

### Windsurf (Devin Desktop)

**Manually: put the files in place**
- File: `.devin/skills/ngs-bcl-to-fastq/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-bcl-to-fastq/SKILL.md

## When to use it
- check an Illumina run folder before demultiplexing
- verify index lengths and i5 orientation in the sample sheet
- run BCL-to-FASTQ conversion with the `--execute` flag
- review demux metrics and the percent undetermined by lane
- record the blocker when `bcl-convert` is not installed

## Example prompts
- Validate the run folder `/data/run` and sample sheet, then show me the demultiplexing plan
- Run BCL-to-FASTQ conversion for `/data/run` into `/data/fastq_out`
- Review metrics after conversion: percent assigned and percent undetermined by lane

## 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: c3e9241779039619.

BEGIN THIRD-PARTY FILE c3e9241779039619
````text
---
name: ngs-bcl-to-fastq
description: Validate Illumina BCL run folders and sample sheets, plan demultiplexing, review index/UMI/lane choices, run BCL-to-FASTQ conversion, and interpret demux metrics while surfacing license/download boundaries.
---

# BCL To FASTQ

Use this skill when the input is an Illumina BCL run folder or the user asks to demultiplex a sequencing run. This is a deep demultiplexing and run-validation skill, not only a command wrapper.

## Essential Inputs

Confirm:

- run folder path with `RunInfo.xml`
- sample sheet path and format
- output directory
- instrument/run metadata from `RunInfo.xml` and `RunParameters.xml`
- lane handling: split by lane or combine lanes
- index mismatch tolerance
- index read structure and dual-index orientation
- UMI layout, if any
- whether adapter trimming/masking should happen during conversion
- whether undetermined reads and demultiplexing metrics should be reviewed before downstream analysis

## Public Tool Boundary

Prefer `bcl-convert` if it is already installed. It is free for local use but proprietary and RPM-distributed by Illumina, so do not auto-download without explicit user approval.

Legacy `bcl2fastq` may exist in older environments. Use it only when BCL Convert is unavailable or the run requires legacy compatibility.

## Preflight

```bash
python plugins/ngs-analysis/scripts/ngs_preflight.py --pipeline bcl_to_fastq --emit-install-plan
```

Also check run-folder structure:

```bash
test -f /path/to/run/RunInfo.xml
test -f /path/to/SampleSheet.csv
find /path/to/run -maxdepth 4 -type d -name BaseCalls
```

## Local Execution Package

Use the plugin-owned runner when the user provides a local run folder and sample sheet:

```bash
python plugins/ngs-analysis/scripts/run_bcl_to_fastq.py \
  --run-folder /path/to/run \
  --sample-sheet /path/to/SampleSheet.csv \
  --output-directory /path/to/fastq_out
```

Add `--execute` only when conversion is requested. The runner validates `RunInfo.xml`, optional `RunParameters.xml`, the BaseCalls directory, sample-sheet rows, duplicate lane/index combinations, and index length compatibility. With `--execute`, it uses installed `bcl-convert`, then legacy `bcl2fastq` if available; if neither exists, it records the blocker instead of downloading proprietary software.

## Validation Checklist

Before conversion, validate:

- `RunInfo.xml` exists and its read structure matches the expected sequencing design.
- `SampleSheet.csv` exists, is the intended version, and has no duplicate sample/index combinations within each lane.
- Index sequence lengths match the index reads and any trimming/masking requested by the sample sheet.
- Dual-index orientation is explicit for the instrument and library prep; do not infer i5 orientation from filenames.
- UMI bases are assigned to the intended read or index read and carried through to FASTQ headers or output metadata as needed.
````
END THIRD-PARTY FILE c3e9241779039619

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