Bioinformatics analysis workflow for viral metagenomic datasets across natural and engineered water systems

This repository contains the bioinformatics workflow and supporting scripts used to process and analyze viral metagenomic sequencing data generated during PhD research at Delft University of Technology. The workflow was applied to viral communities across natural and engineered aquatic systems, including a river–groundwater continuum, wastewater treatment plants, and a riverbank filtration and drinking water treatment system.

The workflow covers sequencing quality control, metagenomic assembly, read mapping, viral contig identification and quality assessment, viral operational taxonomic unit (vOTU) clustering, functional annotation, and taxonomic classification. Major tools include fastp, BBDuk, metaSPAdes, Bowtie2, SAMtools, VirSorter2, DeepVirFinder, CheckV, DRAM-v, Prodigal, and vConTACT2.

The repository contains the main command-line workflow together with supporting R and Python scripts. Raw sequencing data are not duplicated in this repository and are publicly available through the NCBI Sequence Read Archive (SRA). Direct links to the associated NCBI BioProjects are provided in DATA_ACCESS.md.

The code is provided primarily to document the computational workflow and support reproducibility of the associated PhD research. Environment-specific paths have been replaced with portable variables or placeholders and may require adjustment before reuse.