Repeatmasker Tables Custom Part 1

We annotated repeats in assemblies through two rounds of annotation with RepeatMasker4.1.0 (Smit et al. 2020), the first round used custom repeat libraries generated by RepeatModeler2 for each respective assembly and with search engine “ncbi” and option -xsmall. We then converted the softmasked assembly resulting from the first RepeatMasker round to a hardmasked assembly using the lc2n.py script (https://github.com/PdomGenomeProject/repeat-masking), and re-ran RepeatMasker on the hard-masked assembly with RepeatMasker’s internal arthropod repeat library and species “Arthropoda”. We then merged RepeatMasker output tables from both runs to summarize the abundance of RE categories.<br><br><br><i>Authors: John S. Sproul, Scott Hotaling, Jacqueline Heckenhauer, Ashlyn Powell, Amanda M. Larracuente, Joanna L. Kelley, Steffen U. Pauls, and Paul B. Frandsen</i><br>