ngs-bcl-to-fastq Skill
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. Published by openai in plugins.
What is ngs-bcl-to-fastq Skill?
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. Published by openai in plugins. This profile combines repository metadata with install, compatibility, and usage signals so developers can quickly decide whether it fits their agent workflow before opening the source repository.
Automated repository signals based on public metadata such as recency, license, installation evidence, and adoption. These are not a security audit or endorsement.
Key capabilities
- Includes SKILL.md support
- Reusable instructions support
- Data analysis
- Data analysis use cases
Technical details
- Install or run with Copy skill directory
When to use ngs-bcl-to-fastq Skill
- Use it for data analysis.
Built with
Editorial notes
Source
- Creator: openai
- Repository: openai/plugins
- Skill file: plugins/ngs-analysis/skills/ngs-bcl-to-fastq/SKILL.md
What it does
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.
Skill instructions
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
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Frequently asked questions
What is ngs-bcl-to-fastq?
ngs-bcl-to-fastq is a open-source AI agent skill with Copy skill directory. 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.
Who is ngs-bcl-to-fastq best for?
ngs-bcl-to-fastq is best for reusing agent instructions, scripts, and references, data analysis workflows.
How do I install ngs-bcl-to-fastq?
Install or run ngs-bcl-to-fastq using Copy skill directory. Check ngs-bcl-to-fastq for the latest setup command.
Is ngs-bcl-to-fastq actively maintained?
ngs-bcl-to-fastq may need a closer maintenance check before production use.
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