EDTA-Audit: a taxonomy-aware post-processing framework for quality control of EDTA-based transposable element annotation

Summary Batch processing of multiple genome assemblies with EDTA produces numerous result directories that require inspection before downstream analysis. Checking expected output files, reported TE content, and TE-library file sizes individually can be time-consuming. A utility that consolidates these checks can help users identify outputs requiring further review. Results Here, we present EDTA-Audit, a deterministic post-processing screening framework for EDTA outputs. We evaluated EDTA-Audit v1.0.0 using a dataset of 142 plant genome assemblies processed in a concurrent batch-processing setting. Within this dataset, a subset of 13 assemblies was used as a pilot case set to examine the behavior of the default Plant Mode thresholds, and audit outcomes were then summarized across the full dataset. EDTA-Audit assigned PASS or FAIL outcomes and recorded diagnostic reasons for flagged outputs, helping users identify missing required files and unusual TE-content or TE-library profiles requiring troubleshooting or manual inspection. EDTA-Audit consolidates file checks and taxon-informed profile warnings into batch reports, providing a practical first-pass screen to prioritize EDTA outputs for troubleshooting and manual review. Availability and implementation EDTA-Audit v1.0.0, the version used for the analyses reported in this study, was implemented in Bash. The repository has since been updated to a Python-based v2.0.0 implementation, developed with the aim of improving usability, maintainability, and extensibility. All results reported here were obtained using v1.0.0.