Bioinformatics Pipelines and Visualization Working Group Resources

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.

• Rationale
• SARS-CoV-2 Resources
  • Omicron Variant Resources
  • Identifying SARS-CoV-2 Recombinants
  • Bioinformatics Solutions
  • Validation Data Sets
  • Quality Control Guidance
  • Informing Public Health Action
• Monkeypox Resources
  • Bioinformatics Solutions
• Contributing

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.

SARS-CoV-2 recombinants have garnered the attention of the public health community largely due to the unknown clinical and epidemiological implications. This uncertainty emphasizes the need to detect and characterize recombinant SARS-CoV-2 genomes, but the ability to do so rapidly and systematically is not without challenges. Often, recombinant genomes receive an “Unassigned” pango lineage, a non-recombinant pango lineage, or the incorrect recombinant lineage assignment. Additionally, determining the site of recombination within the genome can be difficult for those without extensive SARS-CoV-2 bioinformatics experience.

The PHA4GE Pipelines and Visualization Working Group has created this document as an attempt to highlight critical sources of information and open-source/access resources to aid in the analysis and surveillance of potential recombinant specimens.

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.

In an attempt to assist with quality control (QC) measures, 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 QC challenges for SC2 genomic analysis and suggest a QC systems solutions to address them.

{In development}

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 Mpox genomic analysis and suggest various open-source and freely available bioinformatics resources to address them.

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.