Public Health Alliance for Genomic Epidemiology's repositories
hAMRonization
Parse multiple Antimicrobial Resistance Analysis Reports into a common data structure
pipeline-resources
Bioinformatics Pipeline and Visualization resources
SARS-CoV-2-Contextual-Data-Specification
Collection template and associated materials for SARS-CoV-2 metadata
hAMRonization_workflow
Harmonization of AMR predictor tool outputs
pha4ge.github.io
Static website for the PH4AGE alliance
primer-schemes
Tiling PCR primer scheme definitions
contextual_data_QC_tags
Standardized attributes for labelling sequence datasets with known quality control issues
minimal-pathogen-agnostic-contextual-data-specification
An international minimal metadata standard for public health and One Health genomic surveillance.
Wastewater_Contextual_Data_Specification
A data specification for harmonizing Wastewater pathogen genomics contextual data. The specification provides standardized (ontology-based) fields and terms which are implemented via metadata template(s), supported by field and reference guides as well as different curation and new term request SOPs.
training-resources
Training and workforce development resources
infrastructure-resources
Infrastructure resources
primaschema
Infrastructure for tiled amplicon PCR primer scheme definitions
SARS-CoV-2-Data-Spec-JSON
PHA4GE's SARS-CoV-2 Data Specification Processing Tool
HPAI_Contextual_Data_Specification
This data specification harmonizes contextual data to support H5N1 monitoring with PHA4GE. It provides standardized, ontology-based fields and terms for comprehensive surveillance. Users can implement it via their preferred tools, including DataHarmonizer. Field and reference guides, along with curation and new term request SOPs, support its use.