RetroSeq protocols

View RetroSeq computational protocol

RetroSeq statistics

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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

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Documentation


Maintainer


  • person_outline Thomas M. Keane <>

Publication for RetroSeq

RetroSeq in pipelines

 (4)
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 [] 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 retroseq (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

[…] 49–94), variants were identified visually with the integrated genome viewer (igv v. 2.3.5) (). 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 (; )., we retrieved raw […]

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)., retroseq 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 […]


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RetroSeq in publications

 (24)
PMCID: 5930866
PMID: 29743957
DOI: 10.1186/s13100-018-0120-9

[…] 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 […]

PMCID: 5737362
PMID: 28985298
DOI: 10.1093/gbe/evx170

[…] we annotated 146,268 gaps totaling to 38 mega base pairs (mb) in the polar bear genome; the majority of these gaps (138,041) were >1 bp., reference mapped short reads were processed with retroseq () and mobster () to identify insertions that are present in the corresponding genome while being absent in the reference genome. for retroseq, a minimum mapping quality of 30 and a te […]

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

[…] 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 […]

PMCID: 5850821
PMID: 28486636
DOI: 10.1093/molbev/msx155

[…] and repbase could be classified into 224 unique families (, online, and fasta at www.andersenlab.org/data/laricchia_etal)., 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 […]

PMCID: 5499169
PMID: 28450459
DOI: 10.1534/genetics.116.198895

[…] frequency of one were determined to be causal., 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, […]


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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

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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.