CheckV

CheckV assesses the quality and completeness of single-contig viral genomes assembled from metagenomic datasets and detects and removes host-derived non-viral regions, including integrated proviruses, to improve characterization of viral-encoded functions.

Key Features:

• Automated Quality Assessment: Evaluates quality metrics for single-contig viral genomes derived from metagenomic assemblies.
• Host Contamination Identification: Identifies non-viral regions within integrated proviruses and distinguishes host-derived sequences from viral sequences.
• Completeness Estimation: Estimates genome completeness and categorizes genomes, enabling identification of high-quality genomes (>90% complete).
• Removal of Non-Viral Regions: Identifies and removes non-viral regions to improve assembly accuracy and downstream identification of auxiliary metabolic genes.

Scientific Applications:

• Large-scale viral genome curation: Applied to collections such as IMG/VR and the Global Ocean Virome to curate and assess viral assemblies.
• Viral diversity and completeness assessment: Revealed that many metagenomic viral sequences are small fragments, with only 3.6% classified as high-quality or complete genomes.
• Auxiliary metabolic gene identification: Removal of host contamination improves detection and interpretation of auxiliary metabolic genes and other viral-encoded functions relevant to biogeochemical cycles and ecosystem functioning.

Methodology:

Computationally assesses genome completeness, identifies and removes non-viral regions within integrated proviruses, and was validated using mock datasets before application to large viral genome collections.