Earl Grey: A Fully Automated User-Friendly Transposable Element Annotation and Analysis Pipeline

Transposable elements (TEs) are major components of eukaryotic genomes and are implicated in a range of evolutionary processes. Yet, TE annotation and characterization remain challenging, particularly for nonspecialists, since existing pipelines are typically complicated to install, run, and extract data from. Current methods of automated TE annotation are also subject to issues that reduce overall quality, particularly (i) fragmented and overlapping TE annotations, leading to erroneous estimates of TE count and coverage, and (ii) repeat models represented by short sections of total TE length, with poor capture of 5' and 3' ends. To address these issues, we present Earl Grey, a fully automated TE annotation…

• DF
  Directorate for Biological Sciences
• BA
  Biotechnology and Biological Sciences Research Council

  Awards: BB/M009122/1, BB/N020146/1, BB/N020146/1