A specialized skill for executing genomic analysis pipelines, sequence alignment, and variant calling using industry-standard command-line tools.
Install & Download
1. ClawHub CLI
The fastest way to install a skill directly from the registry.
npx clawhub@latest install bioinformatics
2. Manual Installation
Copy the skill folder to one of these locations
~/.openclaw/skills/ <project>/skills/ Priority: Workspace > Local > Bundled
3. Prompt Installation
Copy this prompt to OpenClaw to install it automatically.
Help me install bioinformatics using Clawhub. If Clawhub is not installed, install it first (npm i -g clawhub).
Prefer to download?
Get the raw skill files in a ZIP archive.
What is Bioinformatics?
The Bioinformatics skill empowers researchers and developers to process complex biological data directly through an AI agent environment. By leveraging Openclaw Skills, users can automate DNA, RNA, and protein sequence analysis while adhering to rigorous scientific standards. This skill acts as a bridge between the agent and powerful low-level binaries, ensuring that genomic workflows are efficient, documented, and reproducible.
Designed for environments running Linux or macOS, the skill manages the entire lifecycle of genomic data—from raw quality control to final variant filtering. It emphasizes local data processing and security, ensuring that sensitive sequence information never leaves the user's local machine while utilizing industry-standard tools like samtools, bwa, and bcftools.
Bioinformatics Use Cases
- Running Quality Control (QC) on raw FASTQ sequencing reads using FastQC and fastp.
- Performing high-throughput sequence alignment to reference genomes such as GRCh38 or GRCm39.
- Executing variant calling pipelines to identify genomic mutations and filtering results by quality.
- Manipulating and converting genomic file formats including BAM, VCF, BED, and FASTA.
- Automating RNA-seq expression analysis and genomic interval operations.
How Bioinformatics Works
- The agent initializes the environment by verifying the presence of required bioinformatics binaries and creating the project directory structure.
- Input data quality is assessed using QC tools to prevent downstream errors from low-quality sequencing reads.
- A specific reference genome is selected and tracked within the local memory to maintain consistency across project tasks.
- Commands are executed through streaming or multi-threaded processes to handle large genomic files without exhausting system resources.
- All transformations, tool versions, and command parameters are logged to ensure the analysis is fully reproducible.
Bioinformatics Setup
To begin using this skill, ensure your environment has the required binaries installed (samtools, bcftools, bwa, etc.).
# Create the local storage directory
mkdir -p ~/bioinformatics/{pipelines,results}
# Install the skill via the hub
clawhub install bioinformatics
Review the setup.md within the skill directory for specific integration guidelines and to initialize the memory.md file for project tracking.
Bioinformatics Data Schema & Taxonomy
The skill maintains a structured taxonomy in ~/bioinformatics/ to manage project state and outputs effectively.
| Path | Purpose |
|---|---|
memory.md |
Persistent storage for project metadata, preferences, and reference genome paths. |
pipelines/ |
Directory containing saved configurations for specific genomic workflows. |
results/ |
Output directory for analysis logs, statistics reports, and processed data files. |
formats.md |
Reference guide for handling coordinate systems (0-based vs 1-based) and file types. |
Bioinformatics Advanced Features
- Resource-aware execution that estimates memory needs and warns users before performing long-running operations.
- Automatic coordinate system handling to prevent off-by-one errors between BED, VCF, and GFF files.
- Support for piped command-line workflows to minimize disk I/O when processing large BAM files.
- Integration with external Openclaw Skills such as data-analysis for advanced statistical interpretation of genomic results.
- Comprehensive logging of tool versions and file checksums to meet scientific reproducibility requirements.
SKILL.md
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