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RetroSeq

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.

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1 user review

1 user review

Daniel's avatar image

Daniel

RetroSeq is user friendly and fairly fast. In my experience, it mapped mobile element insertions (MEI) within 100-200 bp of the actual site.

RetroSeq forum

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RetroSeq classification

RetroSeq specifications

Software type:
Package/Module
Restrictions to use:
None
Output format:
VCF
Computer skills:
Advanced
Requirements:
Bedtools, samtools, Exonerate
Interface:
Command line interface
Output data:
Transposable element calls
Operating system:
Unix/Linux
Stability:
Stable
Maintained:
Yes

RetroSeq distribution

versioning

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No versioning.

RetroSeq support

Documentation

Maintainer

  • Thomas M. Keane <>

Credits

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Publications

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.

Link to literature

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