ArticleMethodsX2026
AquaaG: A comprehensive pipeline for quality assessment and annotation of genomes.
Article in MethodsX, 2026. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Not yet cited in PubMed.
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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4 authors.
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Abstract
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.
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