End-to-End Metagenomic Analysis Platform
Issues • Discussions • Documentation • 中文文档
MICOS-2024 is a comprehensive, production-ready platform for metagenomic analysis that transforms raw sequencing data into actionable biological insights. Built for researchers who need reliability, reproducibility, and ease of use.
| Feature | MICOS-2024 | Traditional Approaches |
|---|---|---|
| Integration | Single unified pipeline | Multiple disconnected tools |
| Reproducibility | Docker + WDL workflows | Manual, error-prone steps |
| Documentation | Comprehensive bilingual guides | Scattered, outdated docs |
| Support | Active community + detailed guides | Limited help resources |
# Clone repository
git clone https://github.com/BGI-MICOS/MICOS-2024.git
cd MICOS-2024
# Deploy with Docker
docker compose -f deploy/docker-compose.example.yml up -d
# Run analysis
python -m micos.cli full-run \
--input-dir data/raw_input \
--results-dir results \
--threads 16 \
--kneaddata-db /path/to/kneaddata_db \
--kraken2-db /path/to/kraken2_db📖 Complete Installation Guide | 安装指南
Raw FASTQ → Quality Control → Taxonomic Profiling →
Diversity Analysis → Functional Annotation → HTML Report
| Module | Tools | Purpose |
|---|---|---|
| Quality Control | FastQC, KneadData | Remove host DNA, trim adapters |
| Taxonomic Profiling | Kraken2, Bracken, Krona | Species classification |
| Diversity Analysis | QIIME2 | Alpha/Beta diversity |
| Functional Annotation | HUMAnN 3.x | Gene families & pathways |
| Reporting | Custom HTML generator | Interactive summaries |
- Speed: Processes 10M reads/sample in ~2 hours
- Scalability: Tested on 1000+ samples
- Parallelization: Multi-threading throughout
| Method | Best For | Setup Time |
|---|---|---|
| Docker | Production, Servers | 5 min |
| Conda | Development, HPC | 15 min |
| Source | Customization | 30 min |
| Document | Description |
|---|---|
| Quick Start | Get running in 5 minutes |
| Installation | Detailed setup instructions |
| User Manual | Complete usage guide |
| Configuration | Parameter reference |
| Troubleshooting | Common issues & solutions |
| 文档 | 描述 |
|---|---|
| 快速开始 | 5分钟上手指南 |
| 安装指南 | 详细安装说明 |
| 用户手册 | 完整使用指南 |
| 配置指南 | 参数参考 |
| 故障排除 | 常见问题与解决 |
| Component | Minimum | Recommended |
|---|---|---|
| OS | Linux/macOS | Linux (Ubuntu 20.04+) |
| CPU | 4 cores | 16+ cores |
| RAM | 16 GB | 32+ GB |
| Storage | 200 GB | 700+ GB SSD |
| Database | Size | Use Case |
|---|---|---|
| Kraken2 Standard | 70 GB | General profiling |
| Kraken2 MiniKraken | 8 GB | Testing/development |
| HUMAnN UniRef90 | 20 GB | Functional analysis |
If you use MICOS-2024 in your research, please cite:
@software{micos2024,
title = {MICOS-2024: Metagenomic Intelligence and Comprehensive Omics Suite},
author = {MICOS-2024 Team},
year = {2024},
url = {https://github.com/BGI-MICOS/MICOS-2024},
version = {1.1.0}
}Also cite the individual tools used in your analysis (Kraken2, HUMAnN, QIIME2, etc.)
| Resource | Link |
|---|---|
| Issues | Report bugs |
| Discussions | Ask questions |
| Releases | Changelog |
| Contributing | Guidelines |
This project is licensed under the MIT License.
MICOS-2024 — Made with ❤️ for the Metagenomics Community