¶ Description
We are compiling a growing list of community-sourced tutorials to conduct bioinformatic analyses of Transposable Elements.
-
Click on the tutorial name to open the dedicated page -
Videos are available for some tutorials, check our YouTube channel
¶ How to contribute
New tutorial submissions are welcomed and encouraged! See here for a quick-start guide.
¶ Available tutorials
| Video | Tutorial name | Software/Method | Description | Type of TE | organism(s) | Author | Date |
|---|---|---|---|---|---|---|---|
| https://www.youtube.com/watch?v=hS7uGfaM_cg | dnaPipeTE intro | dnaPipeTE 1.4c | identification and quantification of transposable elements in raw sequencing reads | All | All | Clément Goubert | 2022-09-02 |
| https://www.youtube.com/watch?v=jDYvbBgX42k | REPET tutorial | REPETv3.0.1 | TE de novo annotation of assembled genomes | All | All | REPET team | 2022-09-21 |
| https://youtu.be/KS7PTKYZk_4 | RepeatExplorer | RepeatExplorer Galaxy Server | Global analysis of repetitive DNA from unassembled sequence reads using RepeatExplorer2 | All | All | RepeatExplorer team | 2022-10-21 |
| https://youtu.be/ZD3tEIttm74 | Manual Annotation by Goubert et al 2022 | various softwares and pipelines | Manual annotation of TEs | All (minus SINEs) | All | Anna V. Protasio | 2022-10-21 |
| https://youtu.be/fem_Jvgunts | How-to guide for running RepeatMasker | RepeatMasker | Repeat annotation | All | All | Jessica Storer | 2022-10-28 |
| https://youtu.be/D1yxNDCeJgs | DFAM | DFAM website and API | Repeat database | All | All | Jessica Storer | 2022-10-28 |
| https://youtu.be/0Z6fYV4voiM | ECCsplorer Mini-Workshop | ECCsplorer | introduction to extrachromosomal circular DNA elements (eccDNAs) and identification of active retrotransposons using eccDNAs | eccDNAs | All | Ludwig Mann | 2022-10-28 |
| A simple pipeline to annotate transposable elements (TEs) in a genome assembly | RepeatModeler2, RepeatMasker | TE de novo annotation of assembled genomes | All | All | Clément Goubert | 2021 | |
| https://www.youtube.com/watch?v=LT6dpFKfHEg | Earl Grey Automated TE Annotation Pipeline | Earl Grey v3.2.1 | Automated de novo curation and annotation of TEs, with TE library refinement and post-annotation defragmentation | All | All | Tobias Baril | 2023-11-13 |