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.
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.
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.
Bioinformatics Solutions for SARS-CoV-2 Genomic Analysis
PHA4GE provides a community-driven, living guide to SARS-CoV-2 genomic analysis, identifying common bioinformatics challenges and open-source resources for public health use. The document supports ongoing collaboration and continuous improvement.
Omicron (B.1.1.529; 21K) Variant Resources
PHA4GE provides a resource-focused guide to support genomic analysis of the SARS-CoV-2 Omicron variant, addressing challenges posed by its mutation profile. The document highlights open-access bioinformatics tools to support public health surveillance and research.
Quality Control Solutions for SARS-CoV-2 Genomic Analysis
PHA4GE provides QC guidance for SARS-CoV-2 genomic sequencing, addressing common sources of variability and data quality issues in NGS workflows. The document highlights practical bioinformatics approaches to support reliable genomic surveillance.