virAnnot

virAnnot analyzes viral metagenomic high-throughput sequencing (HTS) data to assemble reads into contigs, detect conserved viral protein motifs with RPS-Blastn, cluster contigs into OTUs using a 10% sequence identity threshold aligned with ICTV taxonomy, and assign taxonomic annotations via the NCBI taxonomy database.

Key Features:

• Automated OTU Identification: Automates identification of Operational Taxonomic Units (OTUs) from virome data to characterize viral community structure and diversity.
• Read Assembly: Assembles sequencing reads into contigs prior to motif detection and clustering.
• RPS-Blastn Motif Detection: Employs Reverse-Position-Specific BLAST (RPS-Blastn) to detect conserved viral protein motifs within sequencing reads, enhancing sensitivity and specificity of virus detection.
• Clustering by Sequence Identity: Aligns contigs and clusters them based on sequence identity, using a validated 10% sequence identity threshold to group contigs into OTUs consistent with ICTV taxonomy as a proxy for viral species identification.
• Taxonomic Annotation: Provides taxonomic annotation leveraging the NCBI taxonomy database, applicable beyond plant viruses to diverse sequence datasets.

Scientific Applications:

• Viral Diversity Studies: Enables exploration of viral alpha and beta diversity within environmental and host-associated samples through precise OTU identification and clustering.
• Metagenomic Data Analysis: Processes large-scale HTS virome datasets to detect known and putative novel viruses and assess viral community composition.
• Cross-Disciplinary Research: Supports studies in plant virology as well as broader viral ecology and evolution research by providing OTU-based and taxonomy-based interpretations.

Methodology:

The pipeline assembles sequencing reads into contigs, detects conserved motifs using RPS-Blastn, aligns contigs, and clusters them into OTUs based on a 10% sequence identity threshold for taxonomic inference.