HoloVir

HoloVir performs taxonomic and functional characterization of viral metagenomes, with emphasis on data from invertebrate holobionts.

Key Features:

• Optimized Workflow: Employs analyses tested on simulated viral metagenomes with varying diversity and abundance to identify optimal assembly and gene prediction strategies.
• Taxonomic Characterization: Performs pairwise comparisons of single read datasets and predicted gene datasets against the viral RefSeq database for taxonomic assignment.
• Supportive Taxonomic Assignments: Conducts additional comparisons with phage-specific markers and cellular markers to confirm viral origin and detect cellular contamination.
• Broad Functional Classification: Classifies predicted genes into COG categories using EggNOG to provide broad microbial functional insights.
• High-Resolution Functional Analysis: Searches for enrichment of Swiss-Prot keywords within the viral metagenome to identify specific functional attributes.

Scientific Applications:

• Holobiont viral community profiling: Enables taxonomic and functional profiling of viral communities associated with invertebrate holobionts across species, environments, and experimental conditions.
• Empirical case studies: Has been applied to viral metagenomes from the coral Pocillopora damicornis and the sponge Rhopaloeides odorabile.

Methodology:

Workflow components explicitly include testing on simulated viral metagenomes to optimize assembly and gene prediction strategies; pairwise comparisons of reads and predicted genes against viral RefSeq; comparisons with phage-specific and cellular markers; classification of predicted genes via EggNOG COG categories; and searches for Swiss-Prot keyword enrichment.