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Bioinformatics. 2013 Feb 1;29(3):389-90. doi: 10.1093/bioinformatics/bts697. Epub 2012 Dec 10.

RetroSeq: transposable element discovery from next-generation sequencing data.

Author information

1
Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, UK. tk2@sanger.ac.uk

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.

AVAILABILTY:

RetroSeq is open-source and available from https://github.com/tk2/RetroSeq.

PMID:
23233656
PMCID:
PMC3562067
DOI:
10.1093/bioinformatics/bts697
[Indexed for MEDLINE]
Free PMC Article

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