PiRATE: a Pipeline to Retrieve and Annotate Transposable Elements

Date 2018
Author(s) Berthelier JeremyORCID1, Casse Nathalie2, Daccord Nicolas3, Jamilloux Véronique4, Saint-Jean Bruno1, Carrier GregoryORCID1
Affiliation(s) 1 : PBA Laboratory, Ifremer, France
2 : MMS, Université du Mans, France
3 : IRHS, INRA, France
4 : URGI, INRA, France
DOI 10.17882/51795
Publisher SEANOE
Keyword(s) PiRATE, detection, classification, annotation, transposable elements, mobile elements, tool, pipeline, program, transposons, retrotransposon, algae
Abstract

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

Licence CC-BY-NC
User's manual

PiRATE tutorial

Data
File Size Format Processing Access
PiRATE-VM 17 GB OVA Open access
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How to cite 

Berthelier Jeremy, Casse Nathalie, Daccord Nicolas, Jamilloux Véronique, Saint-Jean Bruno, Carrier Gregory (2018). PiRATE: a Pipeline to Retrieve and Annotate Transposable Elements. SEANOE. https://doi.org/10.17882/51795


In addition to properly cite this dataset, it would be appreciated that the following work(s) be cited too, when using this dataset in a publication :


Berthelier Jeremy, Casse Nathalie, Daccord Nicolas, Jamilloux Veronique, Saint-Jean Bruno, Carrier Gregory (2018). A transposable element annotation pipeline and expression analysis reveal potentially active elements in the microalga Tisochrysis lutea. Bmc Genomics, 19(1), 378 (14p.). Publisher's official version : https://doi.org/10.1186/s12864-018-4763-1 , Open Access version : https://archimer.ifremer.fr/doc/00441/55250/