The Silent Hero of COVID-19 Variant Surveillance Effort
summary
A library called StaPH-B docker-builds packages over a hundred open source bioinformatics tools as Docker images so public health labs can run exact versions across on‑prem, cloud, or minimal desktops. Workflows like secret and the Public Health Viral Genomics workflows spin containers per step and hide dependency hell behind WDL/Nextflow GUIs. The pangolin lineage classifier ships updates weekly so images are rebuilt and distributed rapidly and several images exceed one million pulls with earlier spikes of 100–1,000+ pulls in March 2021.
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chapters (7)
- 0:00Start
- 0:41Description of the Field of Bioinformatics
- 1:22Barriers That Prevent the Application of Bioinformatics Techniques in Public Health Laboratories
- 2:15The State Public Health Bioinformatics Working Group
- 3:22Docker Builds
- 7:04Public Health Viral Genomics Workflows
- 9:05The Coronavirus
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