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Annotation and Classification of these elements is a pivotal step in the annotation of each genome. Furthermore, tracing their history can give ample insights into the evolution of a genome and thereby, of a species. Accordingly, different methods for repeat annotation have been developed (A. Smit, Hubley, and Green 2013; Benson 1999; Gymrek et al. 2012). Still, typically they rely on an assembled genome sequence – a prerequisite which can lead to erroneous results. As repetitive elements are highly similar assembly algorithms will collapse repeat variants into a single occurrence or not assemble the repetitive regions at all. Thus, the annotation of repeat regions and thereby the characterization of their content and diversity solely based on an assembled genome sequence can give misleading results.

reper: Genome-wide identification, classification and quantification of repetitive elements without an assembled genome