Fig. 5

The Extensive de-novo TE Annotator (EDTA) pipeline. a The EDTA workflow. LTR retrotransposons, TIR elements, and Helitron candidates are identified from the genome sequence. Sublibraries (such as LTR library, TIR library, etc.) are filtered using EDTA library filtering scripts (including both basic filters and advanced filters, see the “Methods” section for details) for removal of misclassified TEs and are then used to mask TEs in the genome. The unmasked part of the genome is processed by RepeatModeler to identify non-LTR retrotransposons and any unclassified TEs that are missed by the structure-based library. Nested insertions and protein-coding sequences are removed in the final step to generate the final TE library. Performance of b EDTA stage 0 sublibraries and c EDTA stage 1 sublibraries after basic filtering and advanced filtering, respectively. Annotation of the rice genome using d the curated library and e the final EDTA-generated library