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.
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1. 01_EarlGrey_RepeatSummary.csv
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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.
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2. 02_EarlGrey_SummaryFiles.zip
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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.
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3. 03_Rmod_Rmask_SummaryFiles.zip
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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.