TransposonUltimate: software for transposon classification, annotation and detection

MotivationMost genomes harbor a large number of transposons, and they play an important role in evolution and gene regulation. They are also of interest to clinicians as they are involved in several diseases, including cancer and neurodegeneration. Although several methods for transposon identification are available, they are often highly specialised towards specific tasks or classes of transposons, and they lack common standards such as a unified taxonomy scheme and output file format. Moreover, many methods are difficult to install, poorly documented, and difficult to reproduce. ResultsWe present TransposonUltimate, a powerful bundle of three modules for transposon classification, annotation, and detection of transposition events. TransposonUltimate comes as a Conda package under the GPL-3.0 licence, is well documented and it is easy to install. We benchmark the classification module on the large TransposonDB covering over 891,051 sequences to demonstrate that it outperforms the currently best existing solutions. The annotation and detection modules combine sixteen existing softwares, and we illustrate its use by annotating Caenorhabditis elegans, Rhizophagus irregularis and Oryza sativa subs. japonica genomes. Finally, we use the detection module to discover 29,554 transposition events in the genomes of twenty wild type strains of Caenorhabditis elegans. AvailabilityRunning software and source code available on https://github.com/DerKevinRiehl/TransposonClassifierRFSB. Databases, assemblies, annotations and further findings can be downloaded from https://cellgeni.cog.sanger.ac.uk/browser.html?shared=transposonultimate.