RepeatModeler statistics

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RepeatModeler specifications

Information


Unique identifier OMICS_19729
Name RepeatModeler
Software type Application/Script
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Programming languages Perl
License Open Software License v. 2.1
Computer skills Advanced
Version 1.0.10
Stability Stable
Requirements
RepeatMasker & Libraries, RECON, RepeatScout, TRF, NSEG, RMBlast, ABBlast/WUBlast
Maintained Yes

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RepeatModeler in pipelines

 (8)
2018
PMCID: 5886536
PMID: 29621340
DOI: 10.1371/journal.pone.0195461

[…] and combined with 548 repetitive sequences from the repbase database []. the repbase sequences originated from the salmoniformes family, and excluded simple repeats (downloaded january 13, 2017). repeatmodeler v1.0.8 [] was also used together with the allpaths-lg initial assembly in a de novo approach, which identified 1,124 repetitive sequences., the repetitive sequences were then aligned […]

2017
PMCID: 5402704
PMID: 28469420
DOI: 10.1177/1177932217702388

[…] match percentage), -tbf = html + csv (table format), -sort = size (sort field), -rr (flag—create redundancy report), and -trf (flag—create trf-like file)., the first step was preformatted with the repeatmodeler software (default settings) that makes up a pipeline with recon software, repeatscout, repeatmasker, trf, and rmblast, for the de novo identification of tes. the types of long terminal […]

2017
PMCID: 5698052
PMID: 28403535
DOI: 10.1111/pbi.12742

[…] appeared more than once with an average copy number of 1.8. in darmor‐bzh, 26 buscos were missing and five were fragmented, while in tapidor, 31 buscos were missing with an additional 21 fragmented. repeatmodeler identified 310 192 450 bp (36.48%) repeats in darmor‐bzh and 223 636 559 bp (35.15%) repeats in tapidor. ltr/gypsy was the most common repetitive element in both assemblies, with 97 597 […]

2017
PMCID: 5700566
PMID: 29166857
DOI: 10.1186/s12864-017-4296-z

[…] were performed using an in-house pipeline of scripts written in perl and c++. finally, the paired-end and mate-pair reads were assembled using platanus v.1.2.1 []., repeat elements were masked using repeatmodeler v1.0.8 []. recon v1.08 [] and repeatscout v1.0.5 [] were used to perform de novo repeat element prediction. repbase library version 20,140,131 [] was imported to repeatmodeler […]

2017
PMCID: 5905499
PMID: 29253216
DOI: 10.1093/gigascience/gix125

[…] a stepwise strategy for error correction of reads, handling of repetitive sequences, and use of mate-pair libraries., repetitive elements were detected and annotated on the genome assembly with the repeatmodeler de novo repeat family identification and modeling package (repeatmodeler, rrid:scr_015027) []. using recon, repeatscout, and tandem repeat finder, repetitive sequences were detected […]


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RepeatModeler in publications

 (339)
PMCID: 5946483
PMID: 29747580
DOI: 10.1186/s12864-018-4739-1

[…] gaps closure was performed using gapcloser v1.12 [, ]. the completeness of the c. pseudoreteaudii genome was evaluated using cegma []. repeat sequences were identified and classified using repeatmodeler v1.07, repeatproteinmask and repeatmasker v4-0-3., gene structure was predicted using the pasa pipeline with a combination of ab-initio and rna-seq evidence based approaches []. […]

PMCID: 5943715
PMID: 29774047
DOI: 10.3389/fpls.2018.00604

[…] al., ) and others were also obtained by blast search against the rfam database., the repeatmasker (chen, ), repeatproteinmask (http://repeatmasker.org/), tendem repeats finder (trf) (benson, ) and repeatmodeler (smith and hubley, ) were performed to identify repetitive sequences through homolog and de novo prediction. the repeatmasker and repeatproteinmask were used to screen the a. ipaensis […]

PMCID: 5960304
PMID: 29717040
DOI: 10.1073/pnas.1721395115

[…] identified following 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) […]

PMCID: 5916904
PMID: 29695739
DOI: 10.1038/s41598-018-24939-2

[…] applied for dna-level identification using a custom library. at the protein level, repeatproteinmask was used to perform an rmblast search against the te protein database. for de novo prediction, repeatmodeler (http://repeatmasker.org/) and ltr finder were used to identify de novo evolved repeats inferred from the assembled genome., we used the maker2 pipeline to predict protein-coding genes […]

PMCID: 5946948
PMID: 29688346
DOI: 10.1093/gigascience/giy046

[…] with repeatmasker (repeatmasker, version 4.0.3) and repeatproteinmask (from the repeatmasker package) programs with the default parameters []. the de novoapproach used two prediction programs, repeatmodeler [] (version 1.0.7) and ltr-finder [] (version 1.0.5), to build the de novo repeat libraries based on the genome sequences. next, contaminations and multicopy genes were removed […]


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RepeatModeler funding source(s)
Supported by the NIH (R44 HG02244 and R01 HG002939) and the Institute for Systems Biology.

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