RetroSeq specifications

Information


Unique identifier OMICS_00120
Software type Package/Module
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 Bedtools, samtools, Exonerate
Maintained Yes

Versioning


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Documentation


Maintainer


  • person_outline Thomas M. Keane <>

RetroSeq article

RetroSeq citations

 (2)
2016
PMCID: 5069154

[…] of at least 10× coverage across isolates were accepted. tn10 deletions were identified by the absence of reads aligning to the coding section of af162223.1. insertion elements were identified using retroseq35 (fl score of 6 or 8)., we thank d. rudner, r. mazitschek, and r. moellering for helpful insights. we thank j. horn and j. marchionna for custom screening plate manufacture and technical […]

2015
PMCID: 4490562

[…] ncbi sra: erx278110) and our own data (srp020555 and srp046600)., retroseq50 was used to find genomic positions of transposons that are not present in the c. elegans reference genome (wb235). retroseq discovery was run in align mode, using a transposon reference file containing all known tc/mariner-like transposons. a custom script was written to identify those locations that showed […]

RetroSeq institution(s)
Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, UK
RetroSeq funding source(s)
This work was supported by the Medical Research Council, UK and the Wellcome Trust.

RetroSeq review

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Daniel

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Desktop
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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