RepeatModeler2 for automated genomic discovery of transposable element families

The accelerating pace of genome sequencing throughout the tree of life is driving the need for improved unsupervised annotation of genome components such as transposable elements (TEs). Because the types and sequences of TEs are highly variable across species, automated TE discovery and annotation are challenging and time-consuming tasks. A critical first step is the de novo identification and accurate compilation of sequence models representing all of the unique TE families dispersed in the genome. Here we introduce RepeatModeler2, a pipeline that greatly facilitates this process. This program brings substantial improvements over the original version of RepeatModeler, one of the most widely used tools for TE…

• CN
  Canadian Network for Research and Innovation in Machining Technology, Natural Sciences and Engineering Research Council of Canada
• NH
  National Human Genome Research Institute

  Awards: U01-HG009391, U24 HG010136, R01 HG002939
• NI
  National Institute of General Medical Sciences

  Awards: R35-GM122550, R01 GM119125