EDTA¶
Description¶
This package is developed for automated whole-genome de-novo TE annotation and benchmarking the annotation performance of TE libraries. For the initial search of TE candidates, LTRharvest, LTR_FINDER_parallel, and LTR_retriever are incorporated in this package to identify LTR retrotransposons; GenericRepeatFinder, TIR-Learner, and MITE-Hunter are incorporated in this package to identify TIR transposons (a subclass of DNA transposons); HelitronScanner is incorporated in this package to identify Helitron transposons (a subclass of DNA transposons); and finally RepeatModeler is used to identify any TEs missed by these structure-based programs (such as SINEs and LINEs). The EDTA package was designed to filter out false discoveries in raw TE candidates and generate a high-quality non-redundant TE library for whole-genome TE annotations. Selection of initial search programs were based on benckmarkings on the annotation performance using a manually curated TE library in the rice genome.
Environment Modules¶
Run module spider edta to find out what environment modules are available for this application.
Environment Variables¶
- HPC_EDTA_DIR - installation directory
- HPC_EDTA_BIN - executable directory
Citation¶
If you publish research that uses edta you have to cite it as follows:
Categories¶
genomics