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RepeatRunner specifications


Unique identifier OMICS_27296
Name RepeatRunner
Software type Application/Script
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Computer skills Advanced
Stability Stable
Maintained Yes




No version available


  • person_outline Mark Yandell
  • person_outline Barry Moore

Additional information

RepeatRunner citations


Fungal genome and mating system transitions facilitated by chromosomal translocations involving intercentromeric recombination

PLoS Biol
PMCID: 5568439
PMID: 28800596
DOI: 10.1371/journal.pbio.2002527

[…] repetitive elements were then filtered if their coordinates overlapped transposonpsi ( hits (>30% overlap to cds, e-value 1e-10), repeat pfam domains, or repeatrunner [] proteins., the gene set of cbs6039 was also updated using rna-seq data. reads were quality trimmed, jaccard clipped, and normalized using trinity version 2.1.1 []; the filtered reads […]


Genomic innovations linked to infection strategies across emerging pathogenic chytrid fungi

Nat Commun
PMCID: 5364385
PMID: 28322291
DOI: 10.1038/ncomms14742

[…] sets were identified with orthomcl and combined with the evm set. genes were then filtered if >30% coding sequence overlapped tpsi hits (e-value 1e−10), overlapped repeat pfam/tigrfam hits, or repeatrunner proteins., for the updated bd gene calls, the total number predicted remained similar to the previous non-rna-seq-guided set (150 dropped, no new genes added). however, the number […]


Draft Genome of Toxocara canis, a Pathogen Responsible for Visceral Larva Migrans

PMCID: 5266360
PMID: 28095660
DOI: 10.3347/kjp.2016.54.6.751

[…] of 650 bp, and a total length of 53,047 kbp., repetitive elements are ubiquitous in eukaryotic genomes and complicate genome annotation. repeatmasker (version 4.0.5) [] was used in conjunction with repeatrunner [] for repeat identification, characterization, and masking in the 10,853 scaffold sequences that were produced. the repeat libraries used were repbase (version 2014-01–31) [] […]


The draft genome of whitefly Bemisia tabaci MEAM1, a global crop pest, provides novel insights into virus transmission, host adaptation, and insecticide resistance

BMC Biol
PMCID: 5157087
PMID: 27974049
DOI: 10.1186/s12915-016-0321-y

[…] the de novo repeat elements identified by repeatmodeler and the repbase library ( were used to screen the assembled b. tabaci genome using repeatmasker and repeatrunner, which are integrated into the maker annotation pipeline []. miniature inverted-repeat transposable elements (mites) were identified using mite-hunter []., protein-coding genes in the b. […]


The genome of Onchocerca volvulus, agent of river blindness

Nat Microbiol
PMCID: 5310847
PMID: 27869790
DOI: 10.1038/nmicrobiol.2016.216

[…] the maker annotation pipeline consists of four general steps to generate high-quality annotations by taking into account evidence from multiple sources. first, assembled contigs are filtered against repeatrunner, repbase and a species specific repeat library generated by repeat modeler ( using repeatmasker ( to identify […]


The nuclear genome of Rhazya stricta and the evolution of alkaloid diversity in a medically relevant clade of Apocynaceae

Sci Rep
PMCID: 5031960
PMID: 27653669
DOI: 10.1038/srep33782

[…] for genome annotation. repeatmasker (v3-3-0; was used to mask all repeat classes from repbase (, and low complexity sequences. the repeatrunner webserver ( was used to identify transposable elements based on the repeatrunner protein database., the trinity-assembled […]

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