Speaker
Description
Genomic surveillance is crucial for monitoring pathogens of public health significance, focusing on the detection of changes in the pathogens’ genomes, such as new mutations and variants. Prompt detection assists outbreak analytics while revealing variants with increased transmissibility or virulence. The COVID-19 pandemic has underscored the necessity for high-quality genome sequences for effective surveillance.
At the Robert Koch Institute, we are harmonizing our various virus genome reconstruction pipelines into a single multi-virus reconstruction pipeline, Omnifluss, enhancing maintainability and sustainability. We are utilizing the workflow manager Nextflow to ensure scalability, portability, and reproducibility. At the same time, we adhere to nf-core standards for community-driven best practices, guidelines for developing, testing, and curating Nextflow pipelines.
The main processes of Omnifluss are read preprocessing and quality control, variant calling and consensus generation, and post-reconstruction analyses. As a prime example of Omnifluss' utility, we have implemented an Influenza reconstruction pipeline for Illumina short reads, tailored to meet the requirements of Influenza-specific sequencing protocols and the standards set by pathogen experts at the Robert Koch Institute. Its modular architectural structure uses pathogen-specific configurations defining pathogen-specific tools and parameters.
Keywords
genome reconstruction, surveillance, Nextflow
| Registration ID | OHS25-108 |
|---|---|
| Professional Status of the Speaker | PhD Student |
| Junior Scientist Status | Yes, I am a Junior Scientist. |
Authors
External references
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