ViromeScan

ViromeScan characterizes the taxonomy of eukaryotic viruses directly from raw next-generation sequencing (NGS) data to enable sensitive virome profiling and taxonomic assignment.

Key Features:

• Input data: Operates on raw NGS reads from shotgun metagenomic sequencing.
• Hierarchical databases: Leverages hierarchical databases specifically curated for eukaryotic viruses.
• Read-level assignment: Assigns sequencing reads to viral species with high accuracy.
• Speed: Performs taxonomic assignment more than 1000 times faster than other existing methods.
• Denoising: Efficiently denoises samples by removing non-viral microorganism reads, including bacteria, archaea, and eukaryotic microorganisms.
• Body-site profiling: Provides sensitive eukaryotic virome profiling across various human body sites.
• Validation: Has been validated on synthetic microbial communities and metagenomic samples from the Human Microbiome Project.

Scientific Applications:

• Virome taxonomic profiling: Taxonomic characterization of eukaryotic viruses within complex microbial communities such as the intestinal microbiota.
• Host–microbiota interaction studies: Investigation of virus-mediated regulation of host immunophenotype and host–microbiota interactions.
• Viral ecology: Analysis of viral ecology and dynamics within microbiomes.
• Benchmarking and validation: Use in benchmarking metagenomic analyses and validating pipelines with synthetic communities and Human Microbiome Project data.

Methodology:

Processes shotgun metagenomic sequencing data using hierarchical eukaryotic-virus databases and bioinformatic pipelines that assign reads to viral species and denoise non-viral microorganism reads.