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: 1.) Supplementary material data: A) SuppMat_1.xlsx: The genome assembly reference access from Ensembl Plants species used. B) SuppMat_2.docx: A brief transposable elements annotation steps are used in this work. 2.) Code and software: 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).

This work was supported by Fundação Araucária from NAPI Bioinformática (Convênio PDI 66/2021); STIC AmSud (https://www.sticmathamsud.org/stic/presentacion/) Latin America (Brazil, Chile, and Colombia) and France from TELearning Project 2021-22 (21-STIC-13); the PROPPG - UTFPR call 11/2016; and the NVIDIA from the GPU Grant Program 2019 - Accelerated Data Science Call for the GPU Seed Units: Titan V device. DLFP receives a Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES) fellowship (Finance Code 001). TSA receives an undergraduate fellowship from National Council for Scientific and Technological Development (CNPq) - (116568/2018-6).