TransposonUltimate

TransposonUltimate: a holistic bundle of tools for transposon identification

This is the official GitHub page of TransposonUltimate. You will find four pages with powerful tools for transposon identification here:

Transposon Annotation Tools This page contains conda packaged versions of different transposon annotation tools, including MUSTv2, HelitronScanner, SineFinder, MiteTracker, MiteFinderII, SineScan, TirVish, LtrHarvest, TransposonPSI, TransposonNCBICDD1000.
Transposon Classifier "RFSB" This page contains the transposon classification module "RFSB" (Random Forest Selective Binary), that can classify any given DNA sequence into a hierarchical taxonomic scheme. Also, you can use this software to train models for other databases on your own.
Transposon Annotator "reasonaTE" This page contains the transposon annotation pipeline "reasonaTE", that is an ensemble of 13 annotation tools and combines the knowledge of different annotation approaches.
Transposition Event Detector "deTEct" This page contains the transposition event detection module "deTEct", that uses structural variants discovered by Sniffles and PBSV to match these against transposon annotations. As a result, it allows for the observation of potential transposition events.

Materials

Please find all related materials here:

https://cellgeni.cog.sanger.ac.uk/browser.html?shared=transposonultimate/

Please find the TransposonDB as fasta file here:

https://doi.org/10.5281/zenodo.5484069

Citations

Please cite our paper if you find TransposonUltimate useful:

Kevin Riehl, Cristian Riccio, Eric A Miska, Martin Hemberg, TransposonUltimate: software for transposon classification, annotation and detection, Nucleic Acids Research, 2022; gkac136, https://doi.org/10.1093/nar/gkac136

@article{riehl2022transposonultimate,
  title={TransposonUltimate: software for transposon classification, annotation and detection},
  author={Riehl, Kevin and Riccio, Cristian and Miska, Eric and Hemberg, Martin},
  journal={Nucleic Acids Research},
  year={2022}
}

Acknowledgements

We would like to thank Sarah Buddle, Simone Procaccia, Fu Xiang Quah and Alexandra Dallaire for their assistance with testing and debugging the software.

DerKevinRiehl / TransposonUltimate

TransposonUltimate