AquaaG: A comprehensive pipeline for quality assessment and annotation of genomes

The rapid expansion of publicly available genome assemblies has made genome annotation an increasingly challenging task, particularly for large-scale analyses across prokaryotic and eukaryotic organisms. While several tools exist for assembly evaluation and annotation, their use often involves fragmented workflows that require extensive manual coordination. To overcome this limitation, we introduce AquaaG, an automated and reproducible genome annotation pipeline. AquaaG integrates genome assembly retrieval from NCBI, assembly quality assessment using QUAST, organism-specific annotation using Prokka for prokaryotes and BRAKER3 for eukaryotes, gene-space completeness evaluation using BUSCO, and functional annotation using EggNOG-mapper. The pipeline is configured through simple YAML files and supports species-level, kingdom-level, and custom assembly-based analyses with optional submitter-based filtering. AquaaG therefore provides a practical and reproducible framework for high-throughput genome annotation and assessment. The various features of the ‘AquaaG’ are as follows: 1. Genome annotation workflow : AquaaG automates genome retrieval, quality assessment with QUAST, and organism-specific annotation using Prokka and BRAKER3. 2. Configurable analysis modes: The pipeline supports species-wise, kingdom-wise, and assembly-list-based analyses, with optional submitter-based filtering. 3. Comprehensive outputs: AquaaG produces annotated genomes, BUSCO completeness reports, assembly quality reports, and metadata for downstream analyses.