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Official release of EDTA
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@oushujun oushujun released this 27 Dec 07:53
· 531 commits to master since this release
v1.7.0
aa947a2

After a couple months' public testing and solving dozens of issues, EDTA has matured to a point that is worth an official release. Thank you all for your bug reports and feature requests.

Summary of functions and features

  1. Identify high-quality structurally intact TEs including LTR retrotransposons, TIR transposons, and Helitrons.
  2. Reduce false classifications and nested insertions between intact TEs to create a homogenized TE library.
  3. Accept user input TE library to identify novel TEs.
  4. Accept user input CDS to remove gene sequences in the TE library.
  5. Exclude user-specified genomic regions (i.e., gene regions) from TE masking.
  6. Perform whole-genome TE annotation and produce a gff file with both structurally intact and homology-based TE annotations.
  7. Produce self-evaluation results for users to check annotation consistency.
  8. Automatic checkpointing, so that EDTA can automatically start from where it was interrupted.
  9. Multithreading-enabled. Analyzing a maize genome (2.3 Gb, >85% TE) takes less than a week (-threads 36).
  10. Include a companion benchmarking pipeline for developers and researchers to test the annotation quality of custom TE libraries.

Citation

Please cite our paper if you find EDTA is useful:

Ou S., Su W., Liao Y., Chougule K., Ware D., Peterson T., Jiang N.✉, Hirsch C. N.✉ and Hufford M. B.✉ (2019). Benchmarking Transposable Element Annotation Methods for Creation of a Streamlined, Comprehensive Pipeline. Genome Biol. 20(1): 275.

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