Introduction to BioMaster

BioMaster is an advanced, multi-agent framework designed to automate and manage complex bioinformatics workflows using Large Language Models (LLMs), task decomposition, and retrieval-augmented knowledge integration.

By simulating expert-level reasoning and execution, BioMaster enables fast, reproducible, and accurate analysis across various omics modalities — all without requiring extensive programming skills.

Key Capabilities

  • 🧠 Multi-Agent Collaboration Specialized agents (Plan, Task, Check, and Debug) work cooperatively to handle planning, execution, validation, and automatic error recovery.

  • ⚡ Fully Automated Pipelines From raw data to final results, BioMaster manages the entire bioinformatics pipeline, including quality control, alignment, quantification, and downstream analysis.

  • 🔍 Retrieval-Augmented Generation (RAG) Combines preloaded domain knowledge and live script/tool documentation to dynamically plan and execute workflows with adaptive flexibility.

  • 💡 Robust Debugging & Self-healing Execution Automatically detects failed steps and regenerates corrected commands using LLM-powered analysis and error recovery.

  • 🖥️ Interactive GUI A user-friendly web interface allows non-expert users to configure tasks, launch pipelines, and review results intuitively.

  • 🧩 Extensible & Customizable Easily integrates custom scripts, tools, or workflows by updating structured knowledge in PLAN/EXECUTE RAG modules.

Supported Workflows

BioMaster supports a broad spectrum of omics and sequencing workflows, including but not limited to:

  • 🧬 RNA-seq: DEG analysis, splicing, APA, fusion genes, circRNA, functional enrichment

  • 🔬 ChIP-seq: Peak calling, motif discovery

  • 🧫 Single-cell RNA-seq (scRNA-seq): Clustering, marker gene detection

  • 🗺️ Spatial transcriptomics: Cell type annotation, SVG detection, neighborhood analysis

  • 🧩 Hi-C: Mapping, contact matrix construction, loop/TAD detection

  • 🧪 Nanopore & Long-read: Isoform quantification, methylation calling, de novo assembly

  • 🧬 miRNA & specialized assays: miRNA detection, Ribo-seq, Bisulfite-seq, DNase-seq, CAGE-seq, metagenomics, and more

For full details and example workflows, visit the GitHub repository or refer to the RAG knowledge base.

Resources