A standardized pipeline for automated, reproducible bioinformatics analysis including RNA-seq, ChIP-seq, WGS, and differential gene expression.
Install & Download
1. ClawHub CLI
The fastest way to install a skill directly from the registry.
npx clawhub@latest install bioinfo-style
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 bioinfo-style 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 Analysis?
The Bioinformatics Analysis skill brings reproducible, industry-standard genomic workflows directly to your AI development agent. Built on the core principle of prioritizing established, peer-reviewed bioinformatics tools over custom script writing, this workflow guarantees analytical rigor and eliminates the risks of reinventing algorithms from scratch. It automates critical steps from raw quality control through sequence alignment to complex multi-factorial downstream analysis.
By leveraging this architecture within Openclaw Skills, every step of your analytical process is strictly documented into executable shell scripts and aggregated into automated, interactive Rmarkdown visualization reports. This structure ensures that your entire life sciences research data flow remains fully trackable, auditable, and easily reproducible across different execution environments.
Bioinformatics Analysis Use Cases
- Processing raw sequencing reads through automated high-throughput QC pipelines.
- Aligning RNA-seq, ChIP-seq, or Whole Genome Sequencing (WGS) datasets to a reference genome.
- Quantifying feature counts and generating expression matrices from BAM alignments.
- Conducting differential gene expression analysis using robust statistics models.
- Running pathway and functional enrichment analysis including GO, KEGG, and Reactome.
- Creating publication-ready visualizations and integrated HTML analysis reports automatically.
How Bioinformatics Analysis Works
- Environment Initialization: The system activates or dynamically provisions an isolated mamba package environment tailored with exact tools.
- Quality Control: FastQC and processing utilities parse raw input FASTQ sequences and dump metric files to a dedicated QC directory.
- Sequence Alignment & Quantification: Specialized tools like STAR align clean sequences to a reference genome, producing sorted BAM files which featureCounts evaluates into expression matrices.
- Differential Analysis: The workflow populates dynamic Rmarkdown blueprints that compute cross-condition expression differentials using specialized packages like DESeq2.
- Functional Enrichment: Statistical analyses isolate significant gene lists and run hyper-geometric tests against major biological pathway repositories.
- Report Compilation: The workflow compiles the fully localized Rmarkdown codebase into a shareable, polished standalone HTML report complete with embedded plots.
Bioinformatics Analysis Setup
Ensure you have mamba installed on your system. The Openclaw Skills workflow automatically handles environment creation and execution orchestration via bash.
# Standard initialization and environment setup
source ~/.bashrc
# Provision the core bioinformatics stack
mamba create -n bioinfo -c conda-forge -c bioconda \
fastqc trimmomatic star featurecounts deseq2 \
samtools bedtools homer meme
# Activate your newly deployed environment
mamba activate bioinfo
Bioinformatics Analysis Data Schema & Taxonomy
The skill enforces a strict, immutable directory hierarchy to isolate raw data inputs from variable downstream script artifacts. All data transformations must adhere to this standardized layout:
| Directory | Contents | Access Control |
|---|---|---|
raw_data/ |
Original unaltered sequencing files (.fastq.gz) |
Read-Only |
qc_results/ |
Quality control evaluation data from FastQC/MultiQC | Read/Write |
alignment/ |
Reference-mapped output files (.bam, .sam) |
Read/Write |
counts/ |
Normalized structural gene and feature counting matrices | Read/Write |
results/ |
Tabular output from downstream differential analysis | Read/Write |
figures/ |
Rendered plots, heatmaps, and publication graphics | Read/Write |
scripts/ |
Executable Shell and Rmarkdown data processing scripts | Read/Write |
logs/ |
Detailed execution printouts and process error streams | Read/Write |
Bioinformatics Analysis Advanced Features
- Enforces a strict tool-over-code mandate preventing fragile, custom-written algorithms when trusted command line utilities exist.
- Native multi-agent hook patterns seamlessly pipe the output from sequencing scripts into downstream evaluation jobs.
- Automated executable logging pipes every step to shell scripts within the
logs/directory for continuous process tracking. - Integrated parameter validation guarantees that reference files, genomic annotations, and fastq paths exist before consuming compute cores.
- Automated markdown report generation compiles fully interactive HTML outputs featuring cluster charts, volcano plots, and hit matrix heatmaps dynamically.
SKILL.md
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