Manual annotation of transposable elements
According to Goubert et al 2022, see our paper
Tutorial Author(s): Anna V. Protasio
21 Oct 2022:
Manual annotation of transposable elements (TEs) remains the gold standard for in-detail analyses performed on mobile genetic elements and the non-coding genome. It is a labour of love requiring long hours in front of the computer and an acquired "know-how" typically passed from mentor to mentee. We are inpired by the people who taught us how to manually annotate TEs and we thoguht it fair to share this knowledge with the wider world. With our paper we intend to summarise in an easy-to-use and beginner-friendly manner the steps often used to manually annotate TEs. The Supplementary Methods of the said article has a complete tutoral including scrips and detailed explanations of the step-by-step process of manual annotation.
For the manual annotation process per se you can get away with a standard laptop or desktop computer. Most users will use the output of Repeatmodeler to start the manual curation process. However, this is not essential and the process can be initiated with prospective famililes taken from a closely relted organism.
Further details on the software requirements can be found in the Supplementary Methods.
More information about the methods, including alternative access to the manuscript, datasets for running the tutorial, etc. can be found in this Github repo.
For questions about this tutorial, contact Anna Protasio (email address in the paper)