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Research

Guidance Documents & Standards

PHA4GE develops guidance documents, standards, and best-practice resources to support the effective use of genomics in public health. These outputs are created through collaborative working groups and reflect consensus-driven, evidence-based approaches informed by global public health practice.

Our guidance and standards are designed to support public health agencies, laboratories, researchers, and policymakers in strengthening genomic surveillance, data sharing, analysis, and coordinated responses to infectious disease threats.

All documents listed on this page have been developed in collaboration with international partners and contributors, and are intended to be used as practical, adaptable resources across diverse regional and institutional contexts.

How to Use These Resources​

PHA4GE guidance documents and standards may be used to:

  • Inform national and regional public health policies and programmes

  • Support the implementation of genomic surveillance and data workflows

  • Promote consistency, interoperability, and best practice across institutions

  • Complement existing international and national guidelines

Where relevant, documents are updated to reflect emerging evidence, evolving technologies, and feedback from the global public health community.

Other Resources

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MPox Contextual Data Specification

The MPox Contextual Data Specification is an ontology-based, FAIR-aligned framework designed to standardize metadata collection for mpox genomic surveillance. Implemented through the DataHarmonizer platform, the package includes structured collection templates, field and term reference guides, and curation and new term request SOPs to support consistent, interoperable data sharing. Supporting both Canadian and international use cases, the specification enhances data quality, comparability, and collaborative pathogen surveillance across laboratories and public health agencies.

PHA4GE Wastewater Surveillance Guidance and Resources

PHA4GE’s Wastewater Surveillance Working Group provides open guidance and standards addressing surveillance strategies, data analysis, data sharing, and ethical considerations. These living resources support the application of state-of-the-art wastewater surveillance methods in public health practice.

PHA4GE Wastewater Contextual Data Specification

PHA4GE has developed a wastewater contextual data specification to address challenges in harmonising, integrating, and reusing wastewater genomic surveillance data. The standard supports interoperable data exchange across surveillance systems and is extensible to broader environmental and One Health applications.

Ten Best Practices for Public Health Bioinformatics Pipelines

Bioinformatics pipelines are essential for routine genomic analysis in public health, yet the lack of domain-specific best practices has limited reproducibility and interoperability. PHA4GE’s Bioinformatics Pipelines & Visualization Working Group developed ten best practices to guide the development, testing, and maintenance of robust, sustainable pipelines for public health pathogen genomics.

Proposed Standards for Public Health Bioinformatics Software

PHA4GE has developed software development standards to address gaps in reproducibility, interoperability, and sustainability in public health bioinformatics. These guidelines support best practice in the design, testing, and long-term maintenance of bioinformatics software for pathogen genomics.

PHA4GE hAMRonization Tool

PHA4GE has developed an AMR gene detection output standard to address inconsistencies across existing tools and reference databases. Supporting parsers and automated pipelines enable harmonised outputs, benchmarking, and improved reuse of AMR surveillance data.

Bioinformatics Solutions for Mpox Genomic Analysis

PHA4GE provides a community-driven, living guidance document for MPXV genomic analysis, identifying key challenges and open-source bioinformatics tools for public health use. The resource supports ongoing collaboration and updates as methods and tools evolve.

Identifying SARS-CoV-2 Recombinants

PHA4GE provides guidance on identifying and characterising recombinant SARS-CoV-2 genomes, addressing challenges in lineage assignment and breakpoint detection. The document highlights accessible bioinformatics resources to support consistent and systematic recombination surveillance.

COVID-19 Metadata Standard (Template)

PHA4GE developed a SARS-CoV-2 contextual data specification package, implemented through a structured collection template and supporting protocols, to harmonise and support submission of genomic and contextual data to public repositories. Adoption of the standard improves data interoperability, reuse, and integration, and is supported by NCBI’s BioSample database.