To date, 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. In this context, we designed a new bioinformatics pipeline named PiRATE for detect, classify and annotate TEs of non-model organisms. PiRATE combines multiple analysis packages representing all the major approaches for TE detection. The goal is to promote the detection of complete TE sequences of every TE families. The detection of complete TE sequences, bearing recognizable conserved domains or specific motifs, allows to facilitate the classification step. The classification step of PiRATE has been optimized for algal genomes. Each tools used by PiRATE are automated into a stand-alone Galaxy. This PiRATE-Galaxy can be used through a Virtual Machine, which can be download below. This PiRATE-Galaxy is a suitable and flexible platform to study TEs in the genome of every organisms. You can find a tutorial below. Please contact us if you have any issues or comments : berthelier.j [at] laposte.net or gregory.carrier [at] ifremer.fr or you can leave a message on Github:  https://github.com/JBerthelier/PiRATE/issues