RetroSeq is a tool for discovery and genotyping of transposable element variants (TEVs) (also known as mobile element insertions) from next-gen sequencing reads aligned to a reference genome in BAM format. The goal is to call TEVs that are not present in the reference genome but present in the sample that has been sequenced. It should be noted that RetroSeq can be used to locate any class of viral insertion in any species where whole-genome sequencing data with a suitable reference genome is available.
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RetroSeq: transposable element discovery from next-generation sequencing data
Thomas M. Keane, Kim Wong and David J. Adams
Bioinformatics (2013) 29 (3): 389-390.