Accelerating genomics-based surveillance for COVID-19 response in Africa – NCBI
SA’s first SARS-COV-2 genome sequence and analysis – NRF South Africa
A genomics network established to respond rapidly to public health threats in South Africa – NCBI
COVID-19 genome sequencing laboratory network launches in Africa – Africa CDC
COVID-19 analysis – Galaxy
SARS CoV-2 Sequencing – Centers for Disease Control and Prevention, USA
COVID-19 Metadata Standard (Template)
PHA4GE developed a SARS-CoV-2 contextual data specification package, implemented through a structured collection template and supporting protocols, to harmonise and support submission of genomic and contextual data to public repositories. Adoption of the standard improves data interoperability, reuse, and integration, and is supported by NCBI’s BioSample database.
The PHA4GE SARS-CoV-2 Contextual Data Specification for Open Genomic Epidemiology
This publication describes the development of an open, harmonised SARS-CoV-2 contextual data specification extending the INSDC pathogen package. The specification supports interoperable metadata collection, data submission to public repositories, and improved reuse and integration of genomic data for COVID-19 surveillance and research.
Bioinformatics Solutions for SARS-CoV-2 Genomic Analysis
PHA4GE provides a community-driven, living guide to SARS-CoV-2 genomic analysis, identifying common bioinformatics challenges and open-source resources for public health use. The document supports ongoing collaboration and continuous improvement.
Omicron (B.1.1.529; 21K) Variant Resources
PHA4GE provides a resource-focused guide to support genomic analysis of the SARS-CoV-2 Omicron variant, addressing challenges posed by its mutation profile. The document highlights open-access bioinformatics tools to support public health surveillance and research.