This is the code of the initial release of VirDetector. VirDetector is a bioinformatic pipeline for virus surveillance using nanopore sequencing. It can taxonomically classify samples and reconstructs viral genomes, either by using a reference sequence or with an automated hybrid assembly approach. VirDetector then detects the virus present in the sample and uses a selection of sequences to infer phylogenetic trees, separately using maximum likelihood and bayesian inference. It also detects structural variants in the assembled genomes.