Tools & Resources

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The NGS Academy forms part of the Africa CDC Pathogen Genomics Initiative (PGI). This initiative is funded by the Bill & Melinda Gates Foundation. Our training initiatives are carried out in partnership with the African Society for Laboratory Medicine (ASLM).

Tools and Resources


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.

No code Phylogenetic analysis

An open source, free, no-code genomic epidemiology analysis platform for public health