ArticleNature protocols2020
Global analysis of repetitive DNA from unassembled sequence reads using RepeatExplorer2.
Article in Nature protocols, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 191 papers.
What it found
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The trial behind it
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Who cites it
191 citing papers in PubMed.
- Genome evolution of Mediterranean olives following DNA repeats diversification.The plant genome · 2026Article
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- Fusion-Derived Centromeres Reveal Satellite Repeat Remodeling inPlants (Basel, Switzerland) · 2026Article
- Satellite DNAs in Drosophila koepferae (repleta group) reveal patterns of origin, chromosomal organization, transcription, and turnover in the buzzatii cluster.Chromosome research : an international journal on the molecular, supramolecular and evolutionary aspects of chromosome biology · 2026Article
- Detailed re-analysis of satellitome mapping facilitated by the telomere-to-telomere (T2T) assembly of bread wheat genome.Plant molecular biology · 2026Article
- The role of satellite DNAs in repeatome organization and sex chromosome evolution in the owl monkey Aotus infulatus and congeneric species.Biology direct · 2026Article
- Comparative Analysis of Triticeae Satellite Repeats Using Low-Coverage Sequencing, qPCR, and FISH.International journal of molecular sciences · 2026Article
- Comparative genomic analysis and epigenetic profiling of the Drosophila melanogaster B chromosome.Genetics · 2026Article
- A single species, different repeatomes? Genomic plasticity in Passiflora foetida L. complex and comparative insights across the subgenus Passiflora.Chromosome research : an international journal on the molecular, supramolecular and evolutionary aspects of chromosome biology · 2026Article
- Germline-restricted chromosome of songbirds has different centromere compared to regular chromosomes.Heredity · 2026Article
- Satellite DNA evolution in two holocentric species of Edessa true bugs (Hemiptera: Pentatomidae) with unusually high heterochromatin abundance.Chromosome research : an international journal on the molecular, supramolecular and evolutionary aspects of chromosome biology · 2026Article
- Demography and Localized Reservoirs of Diversity Underlie Global Divergence in the Giant Kelp Macrocystis pyrifera.Molecular ecology · 2026Article
- Centromeric tandem repeats expansions in plateau zokor enhance chromosome stability for high-altitude adaptation.Genome biology · 2026Article
- Article
- Genomic and ecological drivers of parallel arid adaptation in tree grapes (Vitaceae).Nature communications · 2026Article
- Nuclear genome profiling of two species ofNAR genomics and bioinformatics · 2026Article
- A new genome assembly of the pea cultivar 'Caméor' provides resources for functional genomics and genetics.Scientific data · 2026Article
- Cytogenomics of Myloplus tiete reveals conserved satellite DNAs since the Late Eocene in Serrasalmidae (Teleostei, Characiformes).Chromosome research : an international journal on the molecular, supramolecular and evolutionary aspects of chromosome biology · 2026Article
- The extraordinary satellitome diversity of freshwater crayfish: a driver of genome evolution.Mobile DNA · 2026Article
- A Deep Dive into Allium Satellite DNAs: Expansion and Characterization of theInternational journal of molecular sciences · 2026Article
131 more citing papers are in PubMed but not listed here.
Corrections and comments
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Authors and funding
3 authors.
Funding
Abstract
RepeatExplorer2 is a novel version of a computational pipeline that uses graph-based clustering of next-generation sequencing reads for characterization of repetitive DNA in eukaryotes. The clustering algorithm facilitates repeat identification in any genome by using relatively small quantities of short sequence reads, and additional tools within the pipeline perform automatic annotation and quantification of the identified repeats. The pipeline is integrated into the Galaxy platform, which provides a user-friendly web interface for script execution and documentation of the results. Compared to the original version of the pipeline, RepeatExplorer2 provides automated annotation of transposable elements, identification of tandem repeats and enhanced visualization of analysis results. Here, we present an overview of the RepeatExplorer2 workflow and provide procedures for its application to (i) de novo repeat identification in a single species, (ii) comparative repeat analysis in a set of species, (iii) development of satellite DNA probes for cytogenetic experiments and (iv) identification of centromeric repeats based on ChIP-seq data. Each procedure takes approximately 2 d to complete. RepeatExplorer2 is available at https://repeatexplorer-elixir.cerit-sc.cz .
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Registered trials
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