This repository hosts PHA4GE-developed guidance documents and resources that address common challenges regarding the integration of bioinformatics solutions for the global public health community.
As public health bioinformatic workflows become increasingly complicated, efforts are needed to promote sensible standardization, portability and reproducibility of assays and workflows across a range of environments, contexts and resource conditions.
The PHA4GE Pipelines and Visualization Working Group has created this document to highlight critical open-source/accesses resources to aid in the understanding and further analysis of the Omicron variant.
In an attempt to assist this integration process, the bioinformatics pipeline and visualization working group of the Public Health Alliance for Genomic Epidemiology (PHA4GE) has drafted this living document to help define the major bioinformatics challenges for SC2 genomic analysis and suggest various open-source and freely available bioinformatics resources to address them.
The US Centers for Disease Control and Prevention's Technical Outreach and Assistance for States Team (TOAST) developed benchmark datasets for SARS-CoV-2 sequencing which are designed to help users at varying stages of building sequencing capacity. Rather than duplicating these efforts, the PHA4GE bioinformatics pipeline and visualization working group will be working alongside TOAST members to maintain and improve upon the currently-available validation datasets.
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Contributions to the documents are more than welcome. To propose a change, edit the source files and open a pull-request with the proposed changes.
If you're interested in participating in further discussions please free to join the Working Group.