A comparative analysis of transposable element diversity and evolution across 75 bee genomes

This readme.txt file was generated on 2025-AUG-06 by Hannah Cook This repository contains files associated with the research article: A comparative analysis of transposable element diversity and evolution across 75 bee genomes by Hannah L. Cook, John S. Sproul, Elizabeth A. Murray, and Silas Bossert For questions and/or concerns please contact the lead author of the paper under hannah.cook1 [at] wsu.edu This repository consists of 3 files. ### 1. 01_EarlGrey_RepeatSummary.csv ### This spreadsheet contains a repeat quantification table from Earl Grey outputs for the genome assemblies of each species. The file is the same as the one provided on the website of the journal. ### 2. 02_EarlGrey_SummaryFiles.zip ### This archive contains Earl Grey's summary files for each of the 81 genome assemblies. Summary files consist of high-level and family-level TE quantification tables, a pie chart of genome repeat content, TE annotations in GFF3 and BED format, repeat landscape plots, and a de novo repeat library in fasta format. Raw data outputs can be made available upon request. ### 3. 03_Rmod_Rmask_SummaryFiles.zip ### This archive contains summary files from the RepeatModeler2 and RepeatMasker pipeline for each of the 81 genome assemblies. The methods used for this pipeline are specified in Rmod_Rmask_methods.pdf. Summary files consist of repeat quantification .tbl outputs from the two rounds of RepeatMasker and a de novo library in fasta format.