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

Genome biology · 2019 · Vol. 20(1) · pp. 275–275

Shujun Ou(Iowa State University)Weija Su(Iowa State University)Yi Liao(University of California, Irvine)Kapeel Chougule(Cold Spring Harbor Laboratory)Jireh Agda(University of Guelph)Adam J. Hellinga(University of Guelph)Carlos Santiago Blanco Lugo(University of Guelph)Tyler A. Elliott(University of Guelph)Doreen Ware(Cornell University)Thomas Peterson(Iowa State University)Ning Jiang✉(Michigan State University)Candice N. Hirsch✉(University of Minnesota)Matthew B. Hufford(Iowa State University)

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Abstract

The benchmarking results and pipeline developed here will greatly facilitate TE annotation in eukaryotic genomes. These annotations will promote a much more in-depth understanding of the diversity and evolution of TEs at both intra- and inter-species levels. EDTA is open-source and freely available: https://github.com/oushujun/EDTA.

Chromosomal and Genetic Variations Genomics and Phylogenetic Studies RNA and protein synthesis mechanismsTransposable elementAnnotationBiologyGenomeRetrotransposonPipeline (software)Computational biologyBenchmarkingGene AnnotationNanopore sequencing