Public Health Genomics in Galaxy
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Welcome to the Galaxy Public Health Community
Public Health Genomics involves the use of genomic information to benefit public health. Whether you’re a researcher, clinician, epidemiologist, or public health professional, the Galaxy Public Health Community invites your participation in building and sharing resources that enhance Galaxy’s utility for public health applications.
Mission
Our mission is to advance public health through genomic data analysis, including:
- Pathogen surveillance and outbreak tracking
- Variant monitoring and characterization
- Antimicrobial resistance (AMR) detection and tracking
- Epidemiological investigations
- Genomic epidemiology and transmission dynamics
- Public health reporting and actionable insights
Community Goals
The Galaxy Public Health Community focuses on:
- Developing and maintaining tools and workflows for public health genomic analysis
- Standardizing best practices for pathogen surveillance and outbreak response
- Fostering collaboration among public health laboratories, researchers, and clinicians
- Supporting interoperability with public health databases and reporting systems
- Expanding training to make genomic surveillance accessible globally
- Promoting FAIR principles in public health data analysis
Public Health Galaxy Servers
Several Galaxy servers worldwide support public health genomic analyses:
Dedicated Public Health Servers
| Server | Institution | Location | URL |
|---|---|---|---|
| GalaxyTrakr | U.S. Food and Drug Administration (FDA) | United States | galaxytrakr.org |
| ARIES | Istituto Superiore di Sanità (ISS) | Italy | Contact ISS for access |
| Sciensano Galaxy | Sciensano | Belgium | Contact Sciensano for access |
| ARTBio | Institut de Biologie Paris Seine (IBPS) | France | mississippi.fr |
| HyPhy | Temple University | United States | hyphy.org |
Organizations Using Galaxy Internally
Many public health institutions use Galaxy for internal genomic surveillance:
- National Institute for Communicable Diseases (NICD) - South Africa
- South African National Bioinformatics Institute (SANBI) - South Africa
- Quadram Institute - United Kingdom
- And many more worldwide…
Want to add your server or organization? Contact us or fill out our interest form.
Getting Started
Training
The Galaxy Training Network (GTN) offers comprehensive tutorials for public health genomic analyses:
Featured Training Topics
- SARS-CoV-2 Data Analysis - Variant calling, consensus building, and lineage assignment
- One Health - 9 tutorials bridging human, animal, and environmental health
- Variant Analysis - 18 tutorials covering SNP/variant calling and interpretation
- Antimicrobial Resistance Detection
- Phylogenetics and Evolution
Community-Maintained Resources
Workflows
The Intergalactic Workflow Commission (IWC) provides peer-reviewed, ready-to-use workflows for public health applications:
Viral Surveillance Workflows
| Workflow | Description | Category |
|---|---|---|
| SARS-CoV-2 Illumina Amplicon (iVar) | Variant calling with Pangolin and Nextclade classification | SARS-CoV-2 |
| SARS-CoV-2 WGS Variant Calling (PE) | Whole genome sequencing variant analysis | SARS-CoV-2 |
| SARS-CoV-2 WGS Variant Calling (SE) | Single-end WGS variant calling | SARS-CoV-2 |
| SARS-CoV-2 ONT ARTIC | Oxford Nanopore ARTIC pipeline | SARS-CoV-2 |
| SARS-CoV-2 Consensus Construction | Build consensus sequences from variants | SARS-CoV-2 |
| SARS-CoV-2 Variation Reporting | Generate variant reports and visualizations | SARS-CoV-2 |
| Influenza A Subtyping | Subtyping and consensus generation for Influenza A | Virology |
| Pox Virus Amplicon Analysis | Analysis of pox virus tiled-amplicon data | Virology |
| Generic Viral Variant Calling | Non-segmented viral genome analysis | Virology |
Bacterial Surveillance Workflows
| Workflow | Description | Category |
|---|---|---|
| AMR Gene Detection | Antimicrobial resistance gene identification | Bacterial Genomics |
| Bacterial Genome Assembly | Shovill-based assembly for bacterial genomes | Bacterial Genomics |
| Bacterial Genome Annotation | Gene, plasmid, and integron detection | Bacterial Genomics |
| cgMLST Typing | Core genome MLST for strain characterization | Bacterial Genomics |
| Bacterial QC Post-Assembly | Quality and contamination assessment | Bacterial Genomics |
| Bacterial QC Raw Reads | Pre-assembly quality control | Bacterial Genomics |
Pathogen Detection & Surveillance
| Workflow | Description | Category |
|---|---|---|
| PathoGFAIR Pathogen Detection | Multi-sample pathogen detection and reporting | Pathogen Detection |
| Allele-based Pathogen ID | Variant-based pathogen identification | Pathogen Detection |
| Gene-based Pathogen ID | Phylogenetic and ARG detection | Pathogen Detection |
Phylogenetics & Epidemiology
| Workflow | Description | Category |
|---|---|---|
| HyPhy Core | Selection analysis (BUSTED, FEL, MEME, PRIME) | Comparative Genomics |
| HyPhy Preprocessing | Codon-aware alignments and phylogenies | Comparative Genomics |
| HyPhy Compare | Contrast-FEL and RELAX analyses | Comparative Genomics |
| CAPHEINE | Combined HyPhy selection analyses | Comparative Genomics |
Metagenomic Surveillance
| Workflow | Description | Category |
|---|---|---|
| Metagenomic Taxonomic & ARG Profiling | Taxonomic classification and ARG detection | Metagenomics |
| Metagenomic Gene Catalog | Gene catalog with functional/taxonomic info | Metagenomics |
| Host Contamination Removal (Short) | Remove human/host reads from samples | Metagenomics |
| Host Contamination Removal (Long) | Nanopore contamination filtering | Metagenomics |
Explore the full workflow library at IWC
Applications in Public Health
The Galaxy Public Health Community resources support diverse applications:
Outbreak Response & Surveillance
- Real-time genomic surveillance of emerging pathogens
- Outbreak investigation and source tracking
- Transmission chain analysis using phylogenetics
- Variant of concern (VOC) monitoring and characterization
Antimicrobial Resistance
- AMR gene detection in clinical and environmental samples
- Resistance mechanism characterization
- Molecular epidemiology of resistant strains
- Treatment guidance through genotype-phenotype prediction
Food Safety
- Foodborne pathogen detection and characterization
- Source attribution in contamination events
- Whole genome sequencing (WGS) for traceback investigations
- Regulatory compliance and reporting
Global Health Security
- Early warning systems for disease threats
- Cross-border surveillance coordination
- One Health integration (human-animal-environment interface)
- Capacity building in resource-limited settings
Get Involved
Communication Channels
- Matrix Channel - Real-time chat and support
- Mailing List - Announcements and discussions
Join Us
We’re building this community and want to hear from you!
📝 Register Your Interest - Add your email to stay informed about:
- Community meetings and events
- New tools and workflows
- Training opportunities
- Collaborative projects
We will add the Google Form URL soon - stay tuned!
How to Contribute
- Subscribe to the mailing list
- Join the Matrix channel
- Share your workflows, tools, or use cases
- Request features or report issues
- Participate in training events and hackathons
Community Coordinators
We are establishing the leadership structure for this community. Interested in helping coordinate? Let us know!
Partner Projects & Collaborations
| Partner | Description | Focus Areas |
|---|---|---|
| PHA4GE | Public Health Alliance for Genomic Epidemiology | Standards, best practices |
| IRIDA | Integrated Rapid Infectious Disease Analysis | Bacterial surveillance platform |
| ABRomics | French National AMR Multi-Omics Platform | AMR research and surveillance |
| GalaxyTrakr | FDA Food Safety Surveillance | Foodborne pathogen tracking |
| Nextstrain | Pathogen genomic epidemiology | Phylodynamics and visualization |
| HyPhy | Molecular evolution analysis | Selection and phylogenetics |
| PathoGFAIR | FAIR pathogen detection | One Health surveillance |
Acknowledgments
We thank the global public health, clinical, and bioinformatics communities working to advance genomic epidemiology and disease surveillance. Special thanks to the Galaxy community for providing the infrastructure and support that makes this work possible.
Publications & Resources
Key Publications Using Galaxy for Public Health
- SARS-CoV-2 Genomic Analysis - Multiple studies leveraging Galaxy workflows for pandemic response
- Foodborne Outbreak Investigations - GalaxyTrakr applications in FDA surveillance
- AMR Surveillance - ABRomics and other platforms using Galaxy infrastructure
- One Health Applications - Integrated human-animal-environmental surveillance
Have a publication to share? Contact us or add it via GitHub.
Ready to get started? Explore our training materials, try our workflows, and join the community!