Bioinformatics Pipelines and Visualization Working Group Resources
Overview
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.
Contents
Rationale
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.
SARS-CoV-2 Resources
Omicron Variant Resources
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.
Identifying SARS-CoV-2 Recombinants
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.
Bioinformatics Solutions
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.
Validation Data Sets
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.
Quality Control Guidance
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.
Informing Public Health Action
{In development}
Mpox Resources
Bioinformatics Solutions
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.
HIV Resources
Bioinformatics Solutions
Understanding the HIV genome, evolutionary dynamics, and subtypes are essential for designing bioinformatic processes. Here, we present a set of resources to help springboard researchers into the world of HIV bioinformatics.
Bioinformatics Development
Public Health Pipeline Best Practices
In an attempt to assist software developers, the Bioinformatics Pipelines and Visualization Working Group of the Public Health Alliance for Genomic Epidemiology (PHA4GE) has proposed a set of best practices, tailored specifically for public health bioinformatics pipelines. These best practices aim to provide a guidance framework for development, testing, maintenance of bioinformatics software. By adhering closely to these best practices, developers can enhance the quality, reliability and sustainability of their software, facilitating impact in public health research.
Contributing
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.