title: RetroSeq: transposable element discovery from next-generation sequencing data.
abstract: A significant proportion of eukaryote genomes consist of transposable element (TE)-derived sequence. These elements are known to have the capacity to modulate gene function and genome evolution. We have developed RetroSeq for detecting non-reference TE insertions from Illumina paired-end whole-genome sequencing data. We evaluate RetroSeq on a human trio from the 1000 Genomes Project, showing that it produces highly accurate TE calls.
  
  
  BACKGROUND
  RetroSeq is open-source and available from https://github.com/tk2/RetroSeq.
authors.affiliation: Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, UK. tk2@sanger.ac.uk
authors.forename: Thomas M
authors.initials: TM
authors.lastname: Keane
authors.forename: Kim
authors.initials: K
authors.lastname: Wong
authors.forename: David J
authors.initials: DJ
authors.lastname: Adams
mesh_terms: D023281:Genomics; D059014:High-Throughput Nucleotide Sequencing; D006801:Humans; D020071:Interspersed Repetitive Sequences; D012984:Software