RetroSeq: Transposable element discovery from next-generation sequencing data

Abstract

Summary: 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.Availabilty: RetroSeq is open-source and available from https://github.com/tk2/RetroSeq. © 2012 The Author.