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.
training-resources
Training and workforce development resources
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.
infrastructure-resources
Infrastructure resources
primaschema
Toolkit for tiling PCR primer scheme definitions
SARS-CoV-2-Data-Spec-JSON
PHA4GE's SARS-CoV-2 Data Specification Processing Tool