drVM

drVM reconstructs complete viral genomes from metagenomic next-generation sequencing (NGS) data to enable detection and characterization of viruses.

Key Features:

• Rapid Viral Read Identification: Uses reference databases of known viral genomes to identify viral reads within metagenomic datasets.
• Genus-Level Read Partitioning: Partitions identified viral reads at the genus level to improve specificity of downstream assembly.
• Read Normalization: Normalizes read coverage to balance representation across different regions of viral genomes prior to assembly.
• De Novo Assembly: Performs de novo assembly to reconstruct complete viral genome sequences from sequencing reads.
• Sequence Annotation and Coverage Profiling: Annotates assembled sequences using reference databases and profiles coverage to assess assembly quality and completeness.
• Validation on Sequencing Platforms: Validated on over 300 sequencing runs generated by Illumina and Ion Torrent platforms.
• Comparative Performance: Reported comparative analyses indicate improved genome completeness and reduced computation time relative to other viral detection tools.

Scientific Applications:

• Virus Discovery and Characterization: Supports discovery and genomic characterization of DNA viruses, RNA viruses, and retroviruses from metagenomic samples.
• Pathogen Identification: Produces complete viral genome sequences from clinical samples to support pathogen identification.
• Epidemiological Studies: Provides assembled viral genomes and coverage data for epidemiological and outbreak investigations.

Methodology:

Viral read identification using reference viral genome databases, genus-level read partitioning, read normalization, de novo assembly, followed by sequence annotation and coverage profiling.