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.
Install
npx skills add openai/plugins --skill ngs-bcl-to-fastqnpx skills add openai/plugins --skill ngs-bcl-to-fastq -a claude-code -gnpx skills add openai/plugins --skill ngs-bcl-to-fastq -a codex -ggemini skills install https://github.com/openai/plugins.git --path plugins/ngs-analysis/skills/ngs-bcl-to-fastqgh skill install openai/plugins ngs-bcl-to-fastqgit clone --depth 1 https://github.com/openai/plugins /tmp/openai__plugins
mkdir -p ~/.claude/skills ~/.agents/skills
cp -R /tmp/openai__plugins/plugins/ngs-analysis/skills/ngs-bcl-to-fastq ~/.claude/skills/ngs-bcl-to-fastq # Claude Code
cp -R /tmp/openai__plugins/plugins/ngs-analysis/skills/ngs-bcl-to-fastq ~/.agents/skills/ngs-bcl-to-fastq # Codex, Cursor, Gemini CLI, Copilot, OpenCode