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

Area of Science:

• Virology
• Bioinformatics
• Genomics

Background:

• The exponential increase in viral sequence data necessitates robust classification systems.
• Existing methods face challenges in accurately classifying diverse viral genomes.

Purpose of the Study:

• To develop and present the Viral Taxonomic Assignment Pipeline (VITAP) for precise viral sequence classification.
• To create a tool that integrates alignment and graph-based approaches for enhanced taxonomic assignment.

Main Methods:

• VITAP integrates alignment-based techniques with graph algorithms for sequence classification.
• The pipeline features an automatically updating database synchronized with International Committee on Taxonomy of Viruses (ICTV) references.
• It can classify viral sequences as short as 1,000 base pairs to the genus level.

Main Results:

• VITAP demonstrates high precision in classifying both DNA and RNA viral sequences, providing confidence levels for taxonomic units.
• The tool achieves high annotation rates across most viral phyla, comparable to existing pipelines.
• Application to deep-sea viromes resulted in significant taxonomic updates and comprehensive diversity insights.

Conclusions:

• VITAP offers an accurate, efficient, and up-to-date solution for viral taxonomic classification.
• The pipeline's generalization capabilities and high annotation rates advance viral discovery, particularly in understudied environments like deep-sea viromes.