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Pathogen genomics


The activities within PHA4GE are aligned to its vision of achieving a rapid global genomic-driven public health response to disease outbreaks. Building the data standards, and sharing best practices require the input from global stakeholders. PHA4GE has defined eight working groups with deliverables determined by public health needs. These include:

Each of these working groups benefit from collaborative work among its members

The PHA4GE group has developed the SARS-CoV-2 Bioinformatics Pipeline and Visualization document with intergrated bioinformatics solutions to support the works of public health laboratories around the world which is available on their github by Libuit KG, Park D, van Heusden P, Neher R, Kapsak CJ, Southgate J, Bridges D, Mboowa G, Lunn S, L. B., et al. (2021). Bioinformatics Solutions for SARS-CoV-2 Genomic Analysis. Retrieved August 16, 2021, from


IDseq is user-friendly software platform, originally developed for metagenomics studies. Functionality has since been added for SC2 consensus assembly calling from paired-end Illumina data.


Basestack is a platform for local deployment of standardized genomic surveillance analysis tools. It currently enables real-time analysis of Nanopore generated sequencing data for SARS-CoV-2.