PHA4GE quality control contextual data tags: standardized annotations for sharing public health sequence datasets with known quality issues to facilitate testing and training
This publication describes the development of standardized contextual data quality-control (QC) tags by PHA4GE to support the responsible sharing and reuse of lower-quality or purpose-specific genomic datasets. Implemented using ontologies and adopted by public health networks such as FDA’s GenomeTrakr, the tags improve dataset discoverability, interpretation, and transparency across public repositories.
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.
hAMRonization: Enhancing antimicrobial resistance prediction using the PHA4GE AMR detection specification and tooling
This publication describes the development of a standardized output specification and the hAMRonization tool to harmonise antimicrobial resistance (AMR) detection results across diverse bioinformatic tools. Developed with international public health laboratories, hAMRonization enables interoperable, unified AMR reporting and supports scalable integration into genomic surveillance workflows.
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.
African scientists are working to pool data that decodes diseases – a giant step
Time and information is of the essence when tackling infectious diseases across countries and continents.
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.
UWC Professor elected to the Royal Society of South Africa
Professor Alan Christoffels, from the University of the Western Cape (UWC), has received the royal stamp of approval following his recent election as a fellow of the Royal Society of South Africa (RSSAf).
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.
The role of pathogen genomics in COVID-19 outbreak response
