PiRATE: a Pipeline to Retrieve and Annotate Transposable Elements
Launch Galaxy
| Virtual Machine: | Pirate Galaxy VM |
|---|---|
| Scope: | Tool Publishing |
| Summary: | Detect, classify and annotate TEs of non-model organisms. |
Comments
- Genome assembly of non-model organisms is usually not at chromosomal level and higly fragmented. This fragmentation is recognized to be, in part, the result of a bad assembly of the transposable elements (TEs) copies, increasing the difficulty to detect and annotate them.
User Support
- PiRATE tutorial
- Email: berthelier.j /at/ laposte.net or gregory.carrier /at/ ifremer.fr
- GitHub Issues
Quotas
- None.
Citations
- Berthelier, J., Casse, N., Daccord, N., Jamilloux, V., Saint-Jean, B., & Carrier, G. (2018). A transposable element annotation pipeline and expression analysis reveal potentially active elements in the microalga Tisochrysis lutea. BMC Genomics, 19, 378. https://doi.org/10.1186/s12864-018-4763-1
- PiRATE tagged publications in the Galaxy Publication Library
Sponsors
- IFREMER