title: LoRTE: Detecting transposon-induced genomic variants using low coverage PacBio long read sequences.
abstract: BACKGROUND
  Population genomic analysis of transposable elements has greatly benefited from recent advances of sequencing technologies. However, the short size of the reads and the propensity of transposable elements to nest in highly repeated regions of genomes limits the efficiency of bioinformatic tools when Illumina or 454 technologies are used. Fortunately, long read sequencing technologies generating read length that may span the entire length of full transposons are now available. However, existing TE population genomic softwares were not designed to handle long reads and the development of new dedicated tools is needed.
  
  
  RESULTS
  LoRTE is the first tool able to use PacBio long read sequences to identify transposon deletions and insertions between a reference genome and genomes of different strains or populations. Tested against simulated and genuineDrosophila melanogasterPacBio datasets, LoRTE appears to be a reliable and broadly applicable tool to study the dynamic and evolutionary impact of transposable elements using low coverage, long read sequences.
  
  
  CONCLUSIONS
  LoRTE is an efficient and accurate tool to identify structural genomic variants caused by TE insertion or deletion. LoRTE is available for download at http://www.egce.cnrs-gif.fr/?p=6422.
authors.affiliation: Laboratoire Evolution, Génomes, Comportement, Ecologie; CNRS, IRD, Université Paris-Saclay, Gif-sur-Yvette, France.
authors.forename: Eric
authors.initials: E
authors.lastname: Disdero
authors.affiliation: Laboratoire Evolution, Génomes, Comportement, Ecologie; CNRS, IRD, Université Paris-Saclay, Gif-sur-Yvette, France.
authors.forename: Jonathan
authors.initials: J
authors.lastname: Filée
keywords: Long read sequence; Population genomic; Structural variation; Transposable element