Upcoming downtime alert: The datacenter hosting MAAGE will be peforming network maintenance which will make the MAAGE site unavailable during a window on Monday, October 19, 2026, from 9-11 a.m. CDT. Compute jobs will not run during that window which means that any job that might overlap it will be held until the network comes back.
Organisms
Genomic Surveillance
Searches
Tools
Workspaces
About

Midwest Alliance for
Applied Genomic Epidemiology

The Midwest Alliance for Applied Genomic Epidemiology (MAAGE) aims to develop a genomic surveillance platform to enhance infectious disease detection and tracking while providing educational resources for public health and healthcare professionals.

Start Bacterial Investigation

Assemble, annotate, and compare bacterial genomes to investigate outbreaks and detect clusters.

Start Viral Investigation

Assemble, annotate, and compare viral genomes to investigate outbreaks and monitor circulating lineages.

Explore Surveillance Data

Browse public genomic surveillance dashboards or build custom dashboards using genome search.

New to MAAGE?

Learn how to navigate MAAGE, organize your data, and begin genomic surveillance and outbreak investigations.

Explore Public Data

Search public genomes, features, AMR phenotypes, and specialty genes across MAAGE's curated databases.

Analyze Your Data

Run bioinformatics analyses on your genomic data using MAAGE's suite of integrated tools.

Getting Started

Start with the data you already have and choose the workflow that best matches your analysis goals.

Comprehensive Genome Analysis Assembly, annotation, AMR, and cgMLST in one pipeline Genome Assembly Assemble raw reads into contigs Taxonomic Classification Classify reads to identify organisms present
Comprehensive Genome Analysis Annotate contigs with AMR, cgMLST, and HierCC Genome Annotation Annotate genomic features using RASTtk Similar Genome Finder Find closely related genomes by Mash distance
Core Genome MLST cgMLST typing and HierCC cluster assignment Phylogenetic Tree Build a codon tree to visualize relationships Whole Genome SNP Analysis Identify SNPs and estimate phylogeny
Gene / Protein Tree Build a tree from selected genes or proteins MSA and SNP Analysis Multiple sequence alignment with variation analysis