VITAP: A High Precision Tool for DNA and RNA Viral Classification Based On Meta-omic Data

Abstract

The rapid growth in the number of newly identified DNA and RNA viral sequences underscores the urgent need for an accurate and comprehensive classification system for all viral realms at different levels. Here, a new Viral Taxonomic Assignment Pipeline (VITAP) is established, which addresses these challenges by integrating alignment-based techniques with graph, offering high precision in classifying both DNA and RNA viral sequences and providing confidence scores 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 1000 base pairs to genus level. VITAP's performance surpasses existing methods in accuracy, precision and recall across all DNA and RNA viral phyla. Its application in deep-sea viromes has led to significant taxonomic updates, providing more comprehensive diversity information of viruses from deep-sea. The VITAP is available at https://github.com/DrKaiyangZheng/VITAP.