A tool for discovery and genotyping of transposable element variants (TEVs) (also known as mobile element insertions) from next-generation 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.
- Software type:
- Package
- Interface:
- Command line interface
- Restrictions to use:
- None
- Output data:
- Transposable element calls
- Output format:
- VCF
- Operating system:
- Unix/Linux
- Computer skills:
- Advanced
- Stability:
- Stable
- Requirements:
- RetroSeq makes use of the bedtools package, samtools, Exonerate, and various common unix tools such as sort and grep.
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RetroSeq is user friendly and fairly fast. In my experience, it mapped mobile element insertions (MEI)…
RetroSeq is user friendly and fairly fast. In my experience, it mapped mobile element insertions (MEI) within 100-200 bp of the actual site.
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Maintainer
- Thomas M. Keane <tk2 at sanger.ac.uk>
Institution(s)
Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, UK
Funding source(s)
This work was supported by the Medical Research Council, UK and the Wellcome Trust.
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(Keane et al., 2013) RetroSeq: transposable element discovery from next-generation sequencing data. Bioinformatics.
PMID: 23233656