RetroSeq statistics

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Citations per year

Number of citations per year for the bioinformatics software tool RetroSeq
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Tool usage distribution map

This map represents all the scientific publications referring to RetroSeq per scientific context
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Associated diseases

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Popular tool citations

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Protocols

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


No version available

Documentation


Maintainer


  • person_outline Thomas M. Keane

Publication for RetroSeq

RetroSeq citations

 (19)
library_books

The case for not masking away repetitive DNA

2018
Mob DNA
PMCID: 5930866
PMID: 29743957
DOI: 10.1186/s13100-018-0120-9

[…] ve DNA from their analysis, even though read mapping technologies have evolved or have been specifically designed to efficiently assay repetitive DNA from whole genome data. These tools include MELT, RetroSeq, EpiTEome and McClintock for TE insertion site identification [–], T-lex to identify presence/absence of TE copies [], Clari-TE to resolve nested TE structure [], TEtoolkit/TEtranscripts for […]

library_books

Phylogenetic Conflict in Bears Identified by Automated Discovery of Transposable Element Insertions in Low Coverage Genomes

2017
Genome Biol Evol
PMCID: 5737362
PMID: 28985298
DOI: 10.1093/gbe/evx170

[…] To our knowledge, only T-lex and T-lex2 (, ) perform Ref+ insertion detection, but they are not compatible with the TeddyPi pipeline due to different file format requirements. Other programs, such as RetroSeq, Mobster and Jitterbug exclusively detect Ref− TE insertions (; ; ). Depending on the mapping-signature utilized for SV-calling (split-reads, read-pairs, depth of coverage) detection results […]

library_books

Insertionally polymorphic sites of human endogenous retrovirus K (HML 2) with long target site duplications

2017
BMC Genomics
PMCID: 5488345
PMID: 28655292
DOI: 10.1186/s12864-017-3872-6

[…] dies, the Illumina whole-genome sequencing (WGS) data obtained from the Cancer Genome Atlas Project, EGS500 project, 1000 Genomes Project, or Human Genome Diversity Project were analyzed using Tea or RetroSeq software to identify LTR-supporting read pairs [, , ]. It is not easy to identify ERVs in repeat regions by mining WGS data because it is necessary to ensure sufficient coverage of the genome […]

library_books

Natural Variation in the Distribution and Abundance of Transposable Elements Across the Caenorhabditis elegans Species

2017
Mol Biol Evol
PMCID: 5850821
PMID: 28486636
DOI: 10.1093/molbev/msx155

[…] The performances of three transposon-detection programs, TEMP (), RetroSeq (), and TE-Locate () were evaluated based on their abilities to detect transposon insertions. These programs were chosen because they each accept BAM/SAM files as inputs and support BWA-MEM a […]

call_split

Experimental Evolution Reveals Favored Adaptive Routes to Cell Aggregation in Yeast

2017
Genetics
PMCID: 5499169
PMID: 28450459
DOI: 10.1534/genetics.116.198895
call_split See protocol

[…] A Ty insertion in the promoter of FLO1 was identified in 12 of the evolved flocculent clones by visual examination in IGV and split read analysis tool retroSeq (). These insertions were verified as full-length using PCR with primers CJA007F/R (Table S4 in File S2). In some cases, an exact breakpoint was determined using the program lumpy, but, for o […]

call_split

Population and clinical genetics of human transposable elements in the (post) genomic era

2017
Mob Genet Elements
PMCID: 5305044
PMID: 28228978
DOI: 10.1080/2159256X.2017.1280116
call_split See protocol

[…] included additional refinement of next-generation sequence based TE insertion calling methods resulting in the Tangram and MELT programs, for the second and third phases of the project, respectively. RetroSeq and Mobster are two of the other most widely used programs for sequence based TE insertion detection. RetroSeq was implemented primarily for the detection of endogenous retrovirus insertions […]


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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's avatar image No country

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.