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A call for benchmarking transposable element annotation methods. 2015
Douglas R Hoen, and
Glenn Hickey, and
Guillaume Bourque, and
Josep Casacuberta, and
Richard Cordaux, and
Cédric Feschotte, and
Anna-Sophie Fiston-Lavier, and
Aurélie Hua-Van, and
Robert Hubley, and
Aurélie Kapusta, and
Emmanuelle Lerat, and
Florian Maumus, and
David D Pollock, and
Hadi Quesneville, and
Arian Smit, and
Travis J Wheeler, and
Thomas E Bureau, and
Mathieu Blanchette
School of Computer Science, McGill University, McConnell Engineering Bldg., Rm. 318, 3480 Rue University, Montréal, Québec H3A 0E9 Canada ; Department of Biology, McGill University, Stewart Biology Bldg., 1205 Ave. du Docteur-Penfield, Montréal, Québec H3A 1B1 Canada.
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.
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