BioSkills

bioSkills

A collection of skills that guide AI coding agents (Claude Code, OpenAI Codex, Google Gemini, OpenClaw) through common bioinformatics tasks.

Project Goal

This repository provides AI agents with expert knowledge for bioinformatics workflows. Each skill contains code patterns, best practices, and examples that help agents generate correct, idiomatic code for common tasks.

Target users range from undergrads learning computational biology to PhD researchers processing large-scale data. The skills cover the full spectrum from basic sequence manipulation to advanced analyses like single-cell RNA-seq and population genetics.

Performance

Evaluation summary report available at [bioskills_eval_20260328.pdf](resources/bioskills_eval_20260328.pdf). Evaluations were performed on the [Bio-Task Bench](https://github.com/GPTomics/bioTaskBench) dataset.


Requirements

Python

• Python 3.9+
• biopython, pysam, cyvcf2, pybedtools, pyBigWig, scikit-allel, anndata

pip install biopython pysam cyvcf2 pybedtools pyBigWig scikit-allel anndata mygene

R/Bioconductor

Required for differential expression, single-cell, pathway analysis, and methylation skills.

if (!require('BiocManager', quietly = TRUE))
    install.packages('BiocManager')
BiocManager::install(c('DESeq2', 'edgeR', 'Seurat', 'clusterProfiler', 'methylKit'))

CLI Tools

# macOS
brew install samtools bcftools blast minimap2 bedtools

# Ubuntu/Debian
sudo apt install samtools bcftools ncbi-blast+ minimap2 bedtools

# conda
conda install -c bioconda samtools bcftools blast minimap2 bedtools \
    fastp kraken2 metaphlan sra-tools bwa-mem2 bowtie2 star hisat2 \
    manta delly cnvkit macs3 tobias

Installation

Claude Code

git clone git@github.com:GPTomics/bioSkills.git
cd bioSkills
./install-claude.sh                              # Install globally
./install-claude.