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 annotating long terminal repeat (LTR) retrotransposons, terminal inverted repeat (T

SUBMITTER: Ou S 

PROVIDER: S-EPMC6913007 | biostudies-literature | 2019 Dec

REPOSITORIES: biostudies-literature