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REPET specifications

Information


Unique identifier OMICS_28131
Name REPET
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Computer skills Advanced
Version 2.5
Stability Stable
Maintained Yes

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Maintainer


  • person_outline Hadi Quesneville

Publication for REPET

REPET citations

 (75)
library_books

Genome wide analysis of the transition to pathogenic lifestyles in Magnaporthales fungi

2018
Sci Rep
PMCID: 5897359
PMID: 29651164
DOI: 10.1038/s41598-018-24301-6

[…] Each of the nine Magnaporthales genomes, plus the genome for Falciphora oryzae, were searched for TEs using the REPET vr. 2.5 pipeline according to the authors’ documentation (https://urgi.versailles.inra.fr/Tools/REPET). The pipeline begins with the TEdenovo script, which uses a series of classifiers to identi […]

library_books

Chinook salmon (Oncorhynchus tshawytscha) genome and transcriptome

2018
PLoS One
PMCID: 5886536
PMID: 29621340
DOI: 10.1371/journal.pone.0195461

[…] posable Element (non-TE) host genes followed by the classification of TEs into the taxa proposed by []. First, BLASTX was used to align repeat library sequences to the protein sequences from both the REPET-formatted RepBase database (v20.05) and the SwissProt UniprotKB database retrieved on January 26th, 2017 []. Repeat library sequences were removed as non-TE host genes if their best hit to a Swi […]

call_split

Integrative analysis of large scale transcriptome data draws a comprehensive landscape of Phaeodactylum tricornutum genome and evolutionary origin of diatoms

2018
Sci Rep
PMCID: 5859163
PMID: 29556065
DOI: 10.1038/s41598-018-23106-x
call_split See protocol

[…] The REPET v2.2 package was used to detect the repetitive fraction of the P. tricornutum genome. The TEdenovo pipeline (https://urgi.versailles.inra.fr/Tools /REPET) was launched including the Repeat Scout […]

library_books

Superior ab initio identification, annotation and characterisation of TEs and segmental duplications from genome assemblies

2018
PLoS One
PMCID: 5851578
PMID: 29538441
DOI: 10.1371/journal.pone.0193588

[…] ences contributed to a consensus. REPET can provide the sequences/genome intervals used to generate the consensus sequences from PILER families, but not for GROUPER or RECON families. Neither RMD nor REPET removes families obtained from gene families as does CARP. REPET will use gene models to filter out gene repeats, but if no gene model intervals are available this is not an option.Neither RMD n […]

library_books

A Near Complete Haplotype Phased Genome of the Dikaryotic Wheat Stripe Rust Fungus Puccinia striiformis f. sp. tritici Reveals High Interhaplotype Diversity

2018
MBio
PMCID: 5821087
PMID: 29463659
DOI: 10.1128/mBio.02275-17

[…] Repeat regions of the primary contigs and haplotigs were predicted independently. We used the REPET pipeline v2.5 (, ) for repeat annotation, in combination with Repbase v21.05 (). First, we used TEdenovo to predict novel repetitive elements following the developer’s instructions and the param […]

library_books

Ten steps to get started in Genome Assembly and Annotation

2018
F1000Res
PMCID: 5850084
PMID: 29568489
DOI: 10.5256/f1000research.14771.r31487

[…] ross_match, ABBlast/WUBlast, RMBlast and Decypher as search engines and uses curated libraries of repeats, currently supporting Dfam (profile HMM library) and Repbase , .Another important tool is the REPET package, one of the most used tools for large eukaryotic genomes with more than 50 genomes analyzed in the framework of international consortia. The REPET package is a suite of pipelines and too […]

Citations

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REPET institution(s)
Unite de Recherche en Genomique-Info, UR 1164, INRA Centre de Versailles-Grignon, Versailles, France; Institut de Mineralogie et de Physique des Milieux Condenses, UMR 7590, CNRS-UPMC-IPGP-Universite Paris Diderot, Paris, France; Genetique, Diversite et Ecophysiologie des Cereales, UMR 1095, INRA Domaine du Crouel, Clermont-Ferrand, France
REPET funding source(s)
Supported by the Institut National de la Recherche Agronomique (INRA) (ASC), the Universite Pierre et Marie Curie (UPMC) (ATER), and by a grant from the Agence Nationale de la Recherche (ANR-05-MMSA-0010).

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