VEBA

VEBA recovers, clusters, and analyzes genomes from metagenomic datasets to enable comprehensive cross-domain genomic characterization of prokaryotic, eukaryotic, and viral organisms.

Key Features:

• End-to-end metagenomic analysis: Integrates genome recovery, genome quality assessment, and taxonomic classification within a single analytical framework.
• Iterative binning procedure: Employs an iterative binning approach with sample-specific and multi-sample frameworks to improve genome recovery accuracy and completeness.
• Consensus microeukaryotic database: Uses a consensus database derived from existing protein databases to optimize microeukaryotic gene modeling and taxonomic classification.
• Clustering-based dereplication strategy: Implements clustering-based dereplication to enable direct comparison of sample-specific genomes and genes across non-overlapping biological samples.
• Candidate Phyla Radiation (CPR) detection: Automates detection of CPR bacteria and applies specialized genome quality assessments for these taxa.
• Modular architecture: Provides modular analytical components that can be executed independently or composed into integrated workflows.

Scientific Applications:

• Biodiversity cataloging: Facilitates recovery and cataloging of genomes across prokaryotic, eukaryotic, and viral domains from environmental samples.
• Novel organism discovery: Supports identification of uncharacterized organisms and genomes lacking public representatives.
• Ecosystem and resilience studies: Enables comparative genomic analyses relevant to ecosystem dynamics and resilience assessments.
• Human and environmental health research: Provides genomic resources for studies linking microbial composition to health and environmental processes.

Methodology:

Iterative binning with sample-specific and multi-sample frameworks; use of a consensus microeukaryotic protein database for gene modeling and taxonomic classification; clustering-based dereplication for cross-sample comparison; automated CPR detection with specialized genome quality assessments; reanalysis of three public datasets recovered 948 MAGs (458 prokaryotic, 8 eukaryotic, 482 viral).