D3234: Pipeline development to accelerate repetitive element analysis in long-read assemblies

Repetitive elements encompass the most dynamic compartments of genomes and account for major variation in genome size, content, and organization, even among closely related species. Studying repeat evolution in a comparative framework that spans populations, species, and diverse clades is a powerful lens for understanding patterns, processes, and mechanisms that underlie genome evolution, repeat biology, and the diversification of life. However, repetitive elements have been historically understudied in diverse non-model groups like many clades of insects relative to their diversity. To help scale repetitive DNA genomics to diverse clades, we are developing a computation pipeline using Snakemake. Our approach wraps widely used repeat analysis software tools RepeatModeler and RepeatMasker and integrates custom scripts to further analyze their output and generate enhanced summaries and figures.