Scripts and data to reproduce figures from our wastewater animal virus surveillance study.
Published article: https://doi.org/10.1016/j.envint.2025.109500
Citation: Mustafa Karatas, Mandy Bloemen, Jill Swinnen, Inge Roukaerts, Steven Van Gucht, Marc Van Ranst, Elke Wollants, Jelle Matthijnssens, Untapped potential of wastewater for animal and potentially zoonotic virus surveillance: Pilot study to detect non-human animal viruses in urban settings, Environment International, Volume 199, 2025, 109500, ISSN 0160-4120, https://doi.org/10.1016/j.envint.2025.109500. (https://www.sciencedirect.com/science/article/pii/S016041202500251X)
├── scripts/ # R scripts for analysis and figure generation
│ ├── Figure_1A.R # Completeness distribution analysis
│ ├── Figure_1B.R # Coverage analysis
│ ├── Figure_1C.R # Sample diversity analysis
│ ├── Figure_2.R # Taxonomic distribution plots
│ ├── Figure_3.R # Phylogenetic analysis
│ └── plot_coverage_zoonosis.R # Coverage plotting utilities
├── input/ # Input data files
│ ├── data.csv # Main dataset with virus detection results
│ └── bam_fasta/ # Reference genomes and mapping files
│ ├── *.fasta # Viral reference sequences
│ ├── *.gff3 # Genome annotations
│ └── bam_mapped.bed # Read mapping coordinates
└── figures/ # Generated publication figures (PDF)
├── Figure1.pdf
├── Figure2.pdf
├── Figure3.pdf
├── Figure4.pdf
├── Figure5.pdf
└── Supplementary_information.pdf
- Ensure R is installed with required packages, see scripts for packages.
- Run scripts individually to regenerate specific figures
- Scripts assume
data.csvis in the working directory
For questions about the code or data, please open an issue on GitHub or you can reach me with my email mustafa.karatas@kuleuven.be
We gratefully acknowledge the support of the Research Foundation – Flanders (FWO) for funding Mustafa Karataş with the PhD Fellowship fundamental research grant (11P7I24N). Additionally, we thank the National Reference Center for their support and providing HEV sequences.