URL: https://github.com/tk2/RetroSeq
Proper Citation: RetroSeq (RRID:SCR_005133)
Description: 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. RetroSeq is a two phase process, the first being the read pair discovery phase where discorandant mate pairs are detected and assigned to a TE class (Alu, SINE, LINE, etc.) by using either the annotated TE elements in the reference and/or aligned with Exonerate to the supplied library of viral sequences.
Abbreviations: RetroSeq
Resource Type: software resource
Defining Citation: PMID:23233656
Keywords: mobile element insertion, next-gen sequencing, bam, transposable element, genome, sequence
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