BUSCO Status Interpretation Guide

Overview

BUSCO (Benchmarking Universal Single-Copy Orthologs) is the standard tool for assessing genome, transcriptome, and proteome completeness by searching for conserved single-copy orthologs from the OrthoDB database. Correct interpretation of BUSCO output is essential for genome quality assessment, comparative genomics, and publication-ready reporting. The most common analytical error is excluding Duplicated BUSCOs from completeness counts, which artificially penalizes polyploid organisms and assemblies with legitimate gene duplications.

This guide covers BUSCO status categories, output file formats, parsing strategies, cross-proteome comparisons, lineage dataset selection, and common pitfalls in BUSCO interpretation.

Key Concepts

BUSCO Status Categories

BUSCO assigns each searched ortholog one of four statuses: