Benchmarking transposable element annotation methods for creation of a streamlined, comprehensive pipeline

Abstract Background Sequencing technology and assembly algorithms have matured to the point that high-quality de novo assembly is possible for large, repetitive genomes. Current assemblies traverse transposable elements (TEs) and provide an opportunity for comprehensive annotation of TEs. Numerous methods exist for annotation of each class of TEs, but their relative performances have not been systematically compared. Moreover, a comprehensive pipeline is needed to produce a non-redundant library of TEs for species lacking this resource to generate whole-genome TE annotations. Results We benchmark existing programs based on a carefully curated library of rice TEs. We evaluate the performance of methods…

• NS
  National Science Foundation

  Awards: IOS-1744001, 1740874, 1744001, IOS-1546727, IOS-1740874, 1546727
• UD
  U.S. Department of Agriculture
• CF
  Canada First Research Excellence Fund
• NI
  National Institute of Food and Agriculture

  Award: IOW05282
• DO
  Division of Molecular and Cellular Biosciences

  Awards: IOS-1744001, IOS-1546727, IOS-1740874
• SO
  State of Iowa