ViroSeek: a viral detection pipeline for second-generation sequencing
Viruses represent a major public health concern, whose emergence is exacerbated by climate change and globalisation. Virome analysis is therefore becoming an important tool for monitoring and managing infectious diseases, but it remains a technical challenge. While several pipelines exist (eg: VirSorter2, VIBRANT, PIMGAVir), their complexity, multiple options and technical requirements cause a lack of accessibility. In this context, we present ViroSeek, a lightweight, reproducible and accessible bioinformatics pipeline specifically designed for the taxonomic analysis of second-generation sequencing data. ViroSeek performs a series of automated steps: quality control (FastQC), sequence trimming (TrimGalore), elimination of non-viral sequences  (BBduk), assembly (SPAdes), taxonomic assignment (Diamond and Taxonkit), relative quantification by remapping reads (minimap2) and removal of PCR duplicates (Samtools). The whole process is designed to produce a clear, usable viral taxonomy table that is suitable for diversity studies. ViroSeek was empirically validated on enriched control samples containing a known panel of viruses. All the expected viruses were correctly detected. Bacterial and host contaminant sequences were effectively removed. One case of weak cross-contamination was also detected, caused by the preparation of the libraries, confirming the sensitivity of the pipeline. The pipeline is freely available and fully documented, supporting its adoption and adaptation by the research community.