PHA4GE SARS CoV 2 Template

The Public Health Alliance for Genomic Epidemiology (PHA4GE)

SARS-CoV-2 Template

The Public Health Alliance for Genomic Epidemiology (PHA4GE) (https://pha4ge.org) is a global coalition that is actively working to establish consensus standards, document and share best practices, improve the availability of critical bioinformatic tools and resources, and advocate for greater openness, interoperability, accessibility and reproducibility in public health microbial bioinformatics.

The PHA4GE template is an international version of the Canadian COVID-19 Genomics Network (CanCOGeN) SARS-CoV-2 contextual data template. It offers standardized fields and terms for a wide range of data types, including repository identifiers and accessions, sample collection and processing information, host information, host vaccination information, host re-infection information, host exposure information, sequencing methods, bioinformatics methods and quality control metrics, lineage and variant information, pathogen diagnostic testing information, provenance and attribution information.

The PHA4GE template enables users to harmonize contextual data to the PHA4GE data standard, validate entered data, and generate public repository-ready contextual data submission forms (including GISAID and NCBI BioSample, SRA, GenBank and GenBank).

Instructions for installation, use and data curation can be found here.

The PHA4GE data specification and other supporting materials can be found here. A preprint describing the specification package is also available and can be found here.