RepeatScout protocols

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RepeatScout specifications

Information


Unique identifier OMICS_03540
Name RepeatScout
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS
Computer skills Advanced
Version 1.0.5
Stability Stable
Maintained Yes

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Publication for RepeatScout

RepeatScout in pipelines

 (8)
2018
PMCID: 5811955
PMID: 29439662
DOI: 10.1186/s12864-018-4516-1

[…] of other 51 species were retrieved from ncbi or ensembl databases [, , , –] (additional file : table s1). the repetitive elements were identified using repeatmodeler 1.0.8 containing recon [] and repeatscout with default parameters []. the derived repetitive sequences were searched against dfam [] and repbase []. if the sequence is classified as “unknown”, they were further searched […]

2016
PMCID: 4752745
PMID: 26873713
DOI: 10.1186/s13073-016-0274-3

[…] filtered to remove sites with a quality score less than 50, less than four reads covering the snp site, and a snp/mapping quality ratio less than 0.75. snps in repeat regions identified using repeatscout [] and mobile genetic elements were excluded. this resulted in 24,660 snps from the core genome. sequence data were deposited in the european nucleotide archive (project accession […]

2016
PMCID: 4833346
PMID: 27082250
DOI: 10.1371/journal.pgen.1005954

[…] asian seabass genome was masked based on known repeats using repeat masker [] and the repbase vertebrate libraries [] (). de novo repeat masking was performed on the genome with windowmasker [] and repeatscout []., a collection of tandem repeats were obtained using tandem repeat finder (trf) version 4.07 [] and post-processed []. the parameters used for the trf search were: maximum mismatch 5; […]

2016
PMCID: 4981986
PMID: 27519651
DOI: 10.1186/s12864-016-2980-z

[…] and not considered for further analysis., genome coverage in genes (cds) and transposable elements was calculated by 500 kb window with an overlap of 50 kb. genes and transposable elements (repet + repeatscout + tallymer) annotations and a karyotype were also needed., the resulting files were formatted to be visualized graphically through the circos software []. a clustering step […]

2011
PMCID: 3049150
PMID: 21333003
DOI: 10.1186/1471-2164-12-120

[…] coding sequences or untranslated adducts to pre-existing operons., the sequence of s. pneumoniae atcc 700669 [] [embl accession code: fm211187] was searched for repeats longer than 50 bp using repeatscout []. for each of the three families identified, multiple sequence alignments were produced with muscle [], which were used to generate hidden markov models (hmm) using hmmer1.8 (more […]


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RepeatScout in publications

 (223)
PMCID: 5960304
PMID: 29717040
DOI: 10.1073/pnas.1721395115

[…] the standard maker-p recipe (weatherby.genetics.utah.edu/maker/wiki/index.php/repeat_library_construction-advanced, accessed october 2015) as described on the gmod site: (i) repeatmodeler with repeatscout v1.0.5, recon v1.08, repeatmasker version open4.0.5, using repbase version 20140131 () and tandemrepeatfinder; (ii) genometools ltrharvest and ltrdigest (); (iii) mitehunter with default […]

PMCID: 5915607
PMID: 29691383
DOI: 10.1038/s41467-018-03423-5

[…] search was used to identify repeat elements in the g. elata genome. for de novo prediction of transposable elements (tes), we used repeatmodeler (http://www.repeatmasker.org/repeatmodeler.html), repeatscout, and ltr-finder with default parameters. for alignment of homologous sequences to identify repeats in the assembled genome, we used repeatproteinmask and repeatmasker […]

PMCID: 5913888
PMID: 29685100
DOI: 10.1186/s12864-018-4680-3

[…] elements using repeatmasker (rm) [] version open-4.0.6 with rmblastn version 2.2.27+ on repbase [] rm database version 20,150,807 (taxon = fungi). de novo repeat families were identified using repeatscout version 1.0.5 []. ltr regions were identified using genometools, suffixerator, ltrharvest (genometools) v1.5.1 (minimum distance 200 bp and maximum distance 5000) and ltrdigest […]

PMCID: 5906906
PMID: 29635287
DOI: 10.1093/gigascience/giy038

[…] rate were investigated in the forest musk deer genome based on two strategies: the library-based strategy of repeatmasker (repeatmasker, rrid:scr_012954) [] and the de novo-based strategy of repeatscout (repeatscout, rrid:scr_014653) []. the forest musk deer genome has large numbers of tes, comprising 42.05% of the genome (), which is similar to those of cattle (46.5%) [] and goats […]

PMCID: 5882950
PMID: 29615780
DOI: 10.1038/s41598-018-23749-w

[…] snap models: aniseed (https://www.aniseed.cnrs.fr/aniseed/)., a de novo repeat library was built for each tunicate genome using repeatmodeler. this utilizes the recon tandem repeats finder from the repeatscout packages to identify species-specific repeats in a genome assembly. repeatmasker was then used to mask those repeats. this repeat library is available on aniseed […]


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RepeatScout institution(s)
Department of Computer Science and Engineering, University of California San Diego La Jolla, CA, USA

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