MICOS-2024

Professional Metagenomic Analysis Platform

End-to-end analysis from raw sequencing data to biological insights.

Core Capabilities

Module	Description	Tools
Quality Control	Host DNA removal and quality filtering	KneadData, FastQC
Taxonomic Profiling	Rapid species classification	Kraken2, Bracken
Diversity Analysis	Alpha/Beta diversity metrics	QIIME2
Functional Annotation	Gene family and pathway analysis	HUMAnN 3.x
Differential Analysis	Statistical comparison of taxa/functions	DESeq2, ALDEx2
Network Analysis	Microbial co-occurrence networks	NetworkX, igraph

Key Features

Containerized — Docker & Singularity support for reproducibility
High Performance — Multi-threading, optimized for large datasets
Rich Visualizations — Interactive HTML reports, Krona charts
Modular Design — Run complete pipeline or individual steps
WDL Workflows — Cromwell-compatible for cloud/HPC deployment

Quick Start

# 1. Clone the repository
git clone https://github.com/LessUp/micos-2024.git
cd micos-2024
 
# 2. Install via Docker (recommended)
docker compose -f deploy/docker-compose.example.yml up -d
 
# 3. Run analysis
python -m micos.cli full-run \
  --input-dir data/raw_input \
  --results-dir results \
  --threads 16

See Installation Guide for details.

Links

Home Installation