Repositories list

• 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 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.

  1•0•0•0•Updated Oct 16, 2024Oct 16, 2024

• Wastewater_Contextual_Data_Specification

  Public
  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.

  MIT License

  •1•4•0•0•Updated Oct 8, 2024Oct 8, 2024

• primaschema

  Public
  Infrastructure for tiled amplicon PCR primer scheme definitions

  Python

  •

  MIT License

  •4•1•18•0•Updated Sep 18, 2024Sep 18, 2024

• primer-schemes

  Public
  Tiling PCR primer scheme definitions

  Creative Commons Attribution 4.0 International

  •4•10•15•1•Updated Sep 4, 2024Sep 4, 2024

• pipeline-resources

  Public
  Bioinformatics Pipeline and Visualization resources

  Apache License 2.0

  •29•54•16•0•Updated Aug 30, 2024Aug 30, 2024

• convAST

  Public
  Python

  •

  MIT License

  •4•1•1•0•Updated Aug 22, 2024Aug 22, 2024

• hAMRonization

  Public
  Parse multiple Antimicrobial Resistance Analysis Reports into a common data structure

  bioinformaticsdata-harmonizationantimicrobial-resistance+ 1parsers

  Python

  •

  GNU Lesser General Public License v3.0

  •30•142•7•0•Updated Aug 8, 2024Aug 8, 2024

• infrastructure-resources

  Public
  Infrastructure resources

  Apache License 2.0

  •1•1•0•0•Updated Jul 17, 2024Jul 17, 2024

• public-health-pipeline-best-practices

  Public
  4•12•2•0•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

  Other

  •9•34•2•1•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

  •3•8•2•0•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

  •3•5•0•1•Updated Oct 27, 2023Oct 27, 2023

• hAMRonization_workflow

  Public
  Harmonization of AMR predictor tool outputs

  file-formatstandardizationantimicrobial-resistance

  Python

  •9•21•3•0•Updated Oct 27, 2023Oct 27, 2023

• SARS-CoV-2-Data-Spec-JSON

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

  Python

  •2•1•1•0•Updated Oct 27, 2023Oct 27, 2023

• training-resources

  Public
  Training and workforce development resources

  Apache License 2.0

  •3•3•0•0•Updated Oct 27, 2023Oct 27, 2023

• pha4ge.github.io

  Public
  Static website for the PH4AGE alliance

  2•13•0•0•Updated Oct 27, 2023Oct 27, 2023