The rapid growth in the number of newly identified DNA and RNA viral sequences underscores the need for an accurate and comprehensive classification system for all viral realms at different taxonomic levels. Here, we establish the Viral Taxonomic Assignment Pipeline (VITAP), which addresses classification challenges by integrating alignment-based techniques with graphs, offering high precision in classifying both DNA and RNA viral sequences and providing confidence level for each taxonomic unit. This tool automatically updates its database in sync with the latest references from the International Committee on Taxonomy of Viruses (ICTV), efficiently classifying viral sequences as short as 1,000 base pairs to genus level. VITAP possesses good generalization capabilities, maintaining accuracy comparable to other pipelines while achieving higher annotation rates across most DNA and RNA viral phyla. Its application in deep-sea viromes has led to significant taxonomic updates, providing comprehensive diversity information of viruses from deep-sea. VITAP is available at
https://github.com/DrKaiyangZheng/VITAP
.
High-throughput sequencing retrieves viral sequences from diverse environments, but these sequences can be difficult to classify. The here developed VITAP is a taxonomic assignment pipeline for DNA and RNA viruses that efficiently classifies incomplete viral sequences (as short as 1000-bp) down to genus level....

VITAP: a high precision tool for DNA and RNA viral classification based on meta-omic data

10.1038/s41467-025-57500-7