Speaker
Description
The SARS-CoV-2 pandemic highlighted the importance of how continuous molecular monitoring remains pivotal for enabling public health interventions. The integrated genomic surveillance (IGS) aims to provide a system in Germany to support both federal and local health authorities across multiple groups of public health relevant pathogens. To address this bioinformatically, we have developed a toolkit of modular computational workflows to enable the genomic assessment of bacterial pathogens.
One major challenge represents the selection of scientific software for inclusion within a routine surveillance system. Many available solutions have been developed for research projects, limiting their applicability for routine public health bioinformatics. This includes limitations in stability, efficiency, speed and license usage, but also the lack of a continuous maintenance strategy.
Here, we present the IGS bioinformatics toolkit, consisting of standardized, curated workflows to address the needs for a continuous surveillance of public health relevant pathogens. The toolkit is open-source and encompasses methods from assembly and profiling, to clustering and visualization of bacterial genomes. These tools may also be utilized for the analysis of additional sources within the One Health framework, including foodborne or veterinary data sets. Our toolkit hereby lays the foundation for performing routine bioinformatic analyses within the scope of the IGS for bacterial pathogens in Germany.
Keywords
Bioinformatics, Integrated Genomic Surveillance, Public Health
| Registration ID | 109 |
|---|---|
| Professional Status of the Speaker | Senior Scientist |
| Junior Scientist Status | No, I am not a Junior Scientist. |
Author
Co-authors
External references
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