SummaryDetection and analysis of viral genomes with Nanopore sequencing has shown great promise in the surveillance of pathogen outbreaks. However, the number of virus detection pipelines supporting Nanopore sequencing is very limited. Here, we present VirPipe, a new pipeline for the detection of viral genomes from Nanopore or Illumina sequencing input featuring streamlined installation and customization.Availability and implementationVirPipe source code and documentation are freely available for download athttps://github.com/KijinKims/VirPipe, implemented in Python and Nextflow.