brycewang-stanford ClawBio Guide
Overview
ClawBio is a bioinformatics skill library for OpenClaw that provides pre-built skills for common genomics and biological analysis tasks — sequence alignment, variant calling, differential expression, pathway analysis, and more. Each skill encapsulates best-practice bioinformatics pipelines as conversational agent capabilities, making complex analyses accessible through natural language.
Installation
# Install as OpenClaw plugin
openclaw plugins install @clawbio/clawbio
# Or add to your OpenClaw configuration
# In openclaw.config.json:
{
"plugins": ["@clawbio/clawbio"]
}
Available Skills
| Skill | Pipeline | Description |
|---|---|---|
| sequence-align | BWA/Bowtie2 | Align reads to reference genome |
| variant-call | GATK/BCFtools | Call SNPs and indels |
| rna-seq | STAR + DESeq2 | Differential expression analysis |
| chip-seq | MACS2 + DiffBind | Peak calling and differential binding |
| metagenomics | Kraken2 + Bracken | Taxonomic classification |
| phylogenetics | IQ-TREE + RAxML | Phylogenetic tree construction |
| protein-structure | AlphaFold/ESMFold | Structure prediction |
| pathway-analysis | GSEA + enrichR | Gene set enrichment |
Usage Examples
RNA-Seq Analysis
# Through OpenClaw conversational interface:
# "Analyze differential expression between treated and control
# samples in the data/rnaseq/ directory"
# ClawBio executes:
# 1. Quality control (FastQC)
# 2. Trimming (Trimmomatic)
# 3. Alignment (STAR)
# 4. Quantification (featureCounts)
# 5. Differential expression (DESeq2)
# 6. Visualization (volcano plot, MA plot, heatmap)
# 7. Pathway enrichment (GSEA)
Variant Calling
# "Call variants from the whole-genome sequencing data
# in samples/ against hg38 reference"
# Pipeline:
# 1. Alignment: BWA-MEM2 → sorted BAM
# 2. Preprocessing: MarkDuplicates, BQSR
# 3. Variant calling: GATK HaplotypeCaller
# 4. Filtering: VQSR or hard filters
# 5. Annotation: VEP or SnpEff
# 6. Report: variant statistics, quality metrics
Metagenomics
# "Classify the microbial communities in my 16S/shotgun
# sequencing data and generate taxonomic plots"
# Pipeline:
# 1. Quality filtering (fastp)
# 2. Host decontamination (Bowtie2 vs human)
# 3. Classification (Kraken2 + Bracken)
# 4. Diversity analysis (alpha + beta diversity)
# 5. Differential abundance (LEfSe/ANCOM)
# 6. Visualization (stacked bar, PCoA, heatmap)
Configuration
{
"clawbio": {
"reference_genomes": {
"hg38": "/data/references/hg38/",
"mm39": "/data/references/mm39/",
"custom": "/data/references/custom/"
},
"tools": {
"aligner": "bwa-mem2",
"variant_caller": "gatk",
"quantifier": "featurecounts",
"de_method": "deseq2"
},
"resources": {
"threads": 8,
"memory_gb": 32,
"gpu": false
},
"output": {
"format": ["html_report", "csv", "plots"],
"figures_dpi": 300
}
}
}
Skill Development
# Create custom bioinformatics skills
# SKILL.md template for new analysis types
"""
---
name: my-custom-analysis
description: "Custom bioinformatics analysis skill"
metadata:
openclaw:
category: "domains"
subcategory: "biomedical"
---
# My Custom Analysis
## When to use
Describe when this analysis is appropriate.
## Pipeline Steps
1. Input validation
2. Processing step 1
3. Processing step 2
4. Output generation
## Example Usage
Show conversational examples.
"""
Use Cases
- Genomics pipelines: Standard NGS analysis workflows
- Lab integration: Natural language interface for bioinformatics
- Teaching: Demonstrate analysis pipelines interactively
- Rapid prototyping: Quick exploratory biological analyses
- Reproducibility: Standardized, documented pipelines