Repositories list

• primaschema

  Public

  pha4ge/primaschema’s past year of commit activity
  Infrastructure for tiled amplicon PCR primer scheme definitions

  Python

  •

  MIT License

  •44 forks•11 star•1717 issues•00 pull requests•Updated Mar 27, 2026Mar 27, 2026

• primer-schemes

  Public
  Tiling PCR primer scheme definitions

  Creative Commons Attribution 4.0 International

  •55 forks•1111 stars•1515 issues•22 pull requests•Updated Mar 12, 2026Mar 12, 2026

• wastewater-guidance

  Public
  Apache License 2.0

  •33 forks•1111 stars•11 issue•00 pull requests•Updated Mar 5, 2026Mar 5, 2026

• hAMRonization

  Public

  pha4ge/hAMRonization’s past year of commit activity
  Parse multiple Antimicrobial Resistance Analysis Reports into a common data structure

  bioinformaticsparsersdata-harmonization+ 1

  bioinformaticsparsersdata-harmonizationantimicrobial-resistance

  Python

  •

  GNU Lesser General Public License v3.0

  •3535 forks•176176 stars•44 issues•11 pull request•Updated Feb 26, 2026Feb 26, 2026

• Malaria-Community-Metadata-Standard

  Public
  11 fork•00 stars•00 issues•00 pull requests•Updated Feb 25, 2026Feb 25, 2026

• Mpox-Community-Metadata-Standard

  Public
  00 forks•00 stars•00 issues•00 pull requests•Updated Feb 20, 2026Feb 20, 2026

• Vibrio-Cholera-Community-Metadata-Standard

  Public
  00 forks•00 stars•00 issues•00 pull requests•Updated Feb 18, 2026Feb 18, 2026

• GenEpi-Network-DSDI

  Public
  Data Standards and Data Integration Working Group

  00 forks•00 stars•00 issues•00 pull requests•Updated Feb 5, 2026Feb 5, 2026

• Neonatal-Sepsis-Community-Metadata-Standard

  Public

  pha4ge/Neonatal-Sepsis-Community-Metadata-Standard’s past year of commit activity
  00 forks•00 stars•00 issues•00 pull requests•Updated Feb 5, 2026Feb 5, 2026

• AI-Resource-Landscape

  Public

  pha4ge/AI-Resource-Landscape’s past year of commit activity
  AI resources relevant to pathogen genomics and public health

  GNU General Public License v3.0

  •00 forks•00 stars•00 issues•00 pull requests•Updated Jan 14, 2026Jan 14, 2026

• training-resources

  Public
  Training and workforce development resources

  HTML

  •

  Apache License 2.0

  •1010 forks•55 stars•00 issues•00 pull requests•Updated Jan 13, 2026Jan 13, 2026

• genotyping-specification

  Public
  A data specification for harmonizing microbial typing contextual data. The specification provides standardized (ontology-based) fields and terms which can be im…

  MIT License

  •00 forks•66 stars•00 issues•00 pull requests•Updated Oct 1, 2025Oct 1, 2025

• infrastructure-resources

  Public
  Infrastructure resources

  Apache License 2.0

  •11 fork•44 stars•11 issue•00 pull requests•Updated Aug 24, 2025Aug 24, 2025

• wastewater-contextual-data-specification

  Public
  A data specification for harmonizing Wastewater pathogen genomics contextual data. The specification provides standardized (ontology-based) fields and terms whi…

  MIT License

  •22 forks•77 stars•55 issues•00 pull requests•Updated Mar 4, 2025Mar 4, 2025

• varnish

  Public
  Template for pkgdown site

  SCSS

  •

  Other

  •6161 forks•00 stars•00 issues•00 pull requests•Updated Feb 27, 2025Feb 27, 2025

• hAMRonization-workflow

  Public
  Harmonization of AMR predictor tool outputs

  file-formatstandardizationantimicrobial-resistance

  file-formatstandardizationantimicrobial-resistance

  Python

  •99 forks•2525 stars•44 issues•00 pull requests•Updated Jan 14, 2025Jan 14, 2025

• hpai-contextual-data-specification

  Public
  This data specification harmonizes contextual data to support H5N1 monitoring with PHA4GE. It provides standardized, ontology-based fields and terms for compreh…

  11 fork•00 stars•00 issues•00 pull requests•Updated Oct 16, 2024Oct 16, 2024

• pipeline-resources

  Public
  Bioinformatics Pipeline and Visualization resources

  Apache License 2.0

  •3636 forks•6565 stars•1616 issues•11 pull request•Updated Aug 30, 2024Aug 30, 2024

• convAST

  Public
  Python

  •

  MIT License

  •44 forks•11 star•11 issue•00 pull requests•Updated Aug 22, 2024Aug 22, 2024

• public-health-pipeline-best-practices

  Public
  44 forks•2020 stars•22 issues•00 pull requests•Updated Mar 25, 2024Mar 25, 2024

• sars-cov-2-contextual-data-specification

  Public
  Collection template and associated materials for SARS-CoV-2 metadata

  harmonizationmetadata-standardsars-cov-2

  harmonizationmetadata-standardsars-cov-2

  Other

  •99 forks•3737 stars•33 issues•11 pull request•Updated Oct 27, 2023Oct 27, 2023

• contextual-data-qc-tags

  Public
  Standardized attributes for labelling sequence datasets with known quality control issues

  Python

  •

  MIT License

  •33 forks•88 stars•22 issues•00 pull requests•Updated Oct 27, 2023Oct 27, 2023

• minimal-pathogen-agnostic-contextual-data-specification

  Public
  An international minimal metadata standard for public health and One Health genomic surveillance.

  MIT License

  •33 forks•55 stars•00 issues•11 pull request•Updated Oct 27, 2023Oct 27, 2023

• sars-cov-2-data-spec-json

  Public
  PHA4GE's SARS-CoV-2 Data Specification Processing Tool

  Python

  •22 forks•11 star•11 issue•00 pull requests•Updated Oct 27, 2023Oct 27, 2023

• pha4ge.github.io

  Public
  Static website for the PH4AGE alliance

  22 forks•1313 stars•00 issues•00 pull requests•Updated Oct 27, 2023Oct 27, 2023