In this repository, we deposited support data for the article "An Atlas of Plant Transposable Elements", available at http://apte.cp.utfpr.edu.br/. Here, we included: <strong>1.) Supplementary material data:</strong><br> A) SuppMat_1.xlsx: The genome assembly reference access from Ensembl Plants species used.<br> B) SuppMat_2.docx: A brief transposable elements annotation steps are used in this work. <strong>2.) Code and software: </strong>all script code create, third-party software, how we are used it, are detailed using Arabidopsis thaliana genome as an example in the GitHub: https://github.com/alerpaschoal/apte_pipeline under the MIT license (please see details in licence.txt file). For the third part-software, consult their terms. To report bugs, to ask for help, and to give any feedback, please contact Alexandre R. Paschoal (paschoal@utfpr.edu.br) or Douglas S. Domingues (douglas.domingues@unesp.br).