Benchmark Proposals

The field of TE annotation is in need of a standard set of benchmarks that are widely adopted by the TE community. These benchmarks may be in the form of well-annotated genomes (or portions thereof) or simulated data sets. To accomplish this, we will collect proposals for individual benchmarks. The proposals should be specified using the template below (see also the example of a completed template). Please email your completed proposals along with any data links to Douglas ( for upload to this page, where they will be accessible for review and comment by all. In addition, we are implementing a server to perform benchmarking calculations. Once sufficient proposals have been received and reviewed, we will create a coherent set of benchmarks and publish it in a highly visible journal.

Thank-you all very much for your contribution!
Mathieu Blanchette, Douglas Hoen, Glenn Hickey, and Thomas Bureau

Template (Word) (PDF)         ——         Example (Word) (PDF)          ——         Discussion Notes (PDF)


Wave IMG_2750     impact


Proposal #1

Benchmark for quality assessment of de novo repeat identification and genome annotation.

Florian Maumus and Hadi Quesneville



Proposal #2

Drosophila melanogaster genome

Emmanuelle Lerat



Proposal #3


Arian Smit and Robert Hubley

See also: Transposable Element Benchmarking.


4 Responses to Benchmark Proposals

  1. Douglas Hoen says:

    As we receive your benchmark proposals, we will post them here for review and comment. To view and comment on a proposal, just click on its header (e.g., click on “Proposal #1″).

  2. Douglas Hoen says:

    Florian and Hadi, thanks for getting the ball rolling!

  3. Douglas Hoen says:

    Thanks Emmanuelle!

  4. Douglas Hoen says:

    Thanks Robert and Arian!

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