A call for benchmarking transposable element annotation methods

Douglas R. Hoen, Glenn Hickey, Guillaume Bourque, Josep Casacuberta, Richard Cordaux, Cédric Feschotte, Anna-Sophie Fiston-Lavier, Aurélie Hua-Van, Robert Hubley, Aurélie Kapusta, Emmanuelle Lerat, Florian Maumus, David D. Pollock, Hadi Quesneville, Arian Smit, Travis J. Wheeler, Thomas E. Bureau, Mathieu Blanchette

DNA derived from transposable elements (TEs) constitutes large parts of the genomes of complex eukaryotes, with major impacts not only on genomic research but also on how organisms evolve and function. Although a variety of methods and tools have been developed to detect and annotate TEs, there are as yet no standard benchmarks-that is, no standard way to measure or compare their accuracy. This lack of accuracy assessment calls into question conclusions from a wide range of research that depends explicitly or implicitly on TE annotation. In the absence of standard benchmarks, toolmakers are impeded in improving their tools, annotators cannot properly assess which tools might best suit their needs, and downstream researchers cannot judge how accuracy limitations might impact their studies. We therefore propose that the TE research community create and adopt standard TE annotation benchmarks, and we call for other researchers to join the authors in making this long-overdue effort a success.