RetroSeq protocols

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description
RetroSeq computational protocol

RetroSeq specifications

Information


Unique identifier OMICS_00120
Name RetroSeq
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


Add your version

Documentation


Maintainer


  • person_outline Thomas M. Keane <>

Publication for RetroSeq

RetroSeq IN pipelines

 (6)
2016
PMCID: 4971691
PMID: 27485608
DOI: 10.1186/s12864-016-2847-3

[…] to sort the alignments and then used the command ‘samtools merge’ to merge the alignments from different sequence lanes., to identify candidate non-ref tes with read pair support, we used a modified retroseq [19] workflow, adjusting some alignment methods and parameters for suitability in genome-wide analysis of non-ref tes in crops. first, we checked the bam file, and the alignments […]

2016
PMCID: 5069154
PMID: 27642863
DOI: 10.1038/nchembio.2176

[…] 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 […]

2016
PMCID: 5521736
PMID: 28173099
DOI: 10.1093/gbe/evw286

[…] identified visually with the integrated genome viewer (igv v. 2.3.5) (thorvaldsdottir et al. 2013). potential large-scale insertions due to mobile genetic elements were additionally detected using retroseq (workflow available on github, https://github.com/behrimg/r_toruloides) and a library of all reported fungal mobile elements, created using repbase update v. 20.12 (jurka et al. 2005; keane […]

2015
PMCID: 4490562
PMID: 26077599
DOI: 10.1038/ncomms8394

[…] national institute of genetics japan (ncbi sra: drp001005) from the 50 helminth genome initiative (submitted by the sanger center, 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 […]

2015
PMCID: 4490562
PMID: 26077599
DOI: 10.1038/ncomms8394

[…] 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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Anonymous user #64

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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.