Figure 6.

Workflow of select TE discovery pipelines. Each process in the pipeline has been categorized as classification (purple), signature-based TE detection (green), de novo TE detection (gold), homology-based detection (black), genome annotation (red), filter and/or refinement (blue) and clustering (grey). Arrows indicate the general workflow direction. NOTE: the above image is meant to describe the high-level organization of each pipeline, and does not reflect the inherent complexity contained within. Refer to Supplementary Materials for additional details.