Fig. 8: TEtrimmer exhibits improved genome-wide TE annotation ability in comparison to EDTA and RepeatModeler2.

We assessed the genome TE annotation performance of EDTA, RepeatModeler2 (RM2), and both after additional TEtrimmer analysis (EDTA+TEtrimmer and RM2+TEtrimmer, respectively). All genome-wide TE annotation results based on de novo-generated libraries were compared with the results of the respective TE reference libraries (Table 1). We used a confusion matrix^34,45 to calculate the sensitivity, precision, accuracy, specificity, F1 score, and false discovery rate (FDR) of the tools. The genomes of six organisms were used for the analysis, i.e., B. hordei, D. melanogaster, D. rerio, O. sativa, Z. mays, and H. sapiens. A The bar plots show the sensitivity (green), precision (blue), and F1 score (orange) calculated with a confusion matrix for the six organisms indicated on top of each graph. The x-axis represents the respective analysis tools, and the y-axis displays the metrics score values based on overall genome TE annotation correctness (All TEs) at a range of 0.7 to 1.0. B Detailed genome-wide TE annotation benchmarking for H. sapiens. The radar plots in the upper panels show the benchmarking metrics for LTR retrotransposon (green), LINEs (red), and SINEs (orange). The lower panels display the annotation overlap and differences between de novo-generated TE libraries from the indicated tool (left) and the reference consensus TE library for H. sapiens (right); each bar indicates the number of Mbp masked as the respective element in the genome. The links between the left and right bars indicate the connections between the respective libraries. TE types shown are LTR retrotransposon (green), LINE (red), SINE (orange), DNA transposon (dark blue), unclassified (light blue), and genomic sequence not identified as TE (Not TE; grey). Third-party icons used in this Figure: rice_cartoon icon by Daniel Carvalho (https://figshare.com/authors/Plant_Illustrations/3773596), human_female / Human_male icon (DBCLS https://togotv.dbcls.jp/en/pics.html), and zebrafish_simplified icon by DBCLS are licensed under CC-BY 4.0 Unported (https://creativecommons.org/licenses/by/4.0/); fruitfly_drosophila-yellow icon by Servier (https://smart.servier.com/) and corn icon by Servier (https://smart.servier.com/) are licensed under CC-BY 3.0 Unported (https://creativecommons.org/licenses/by/3.0/). Raw data: Source Data file.