ArticleNucleic acids research2014
RepARK--de novo creation of repeat libraries from whole-genome NGS reads.
Article in Nucleic acids research, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 41 papers.
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Who cites it
41 citing papers in PubMed.
- Streamlining of Simple Sequence Repeat Data Mining Methodologies and Pipelines for Crop Scanning.Plants (Basel, Switzerland) · 2024Review
- Study of Dispersed Repeats in theInternational journal of molecular sciences · 2024Article
- Repetitive DNA sequence detection and its role in the human genome.Communications biology · 2023Review
- Assembly-Free Detection and Quantification of Transposable Elements with dnaPipeTE.Methods in molecular biology (Clifton, N.J.) · 2023Article
- Chromosome-scale assembly with a phased sex-determining region resolves features of early Z and W chromosome differentiation in a wild octoploid strawberry.G3 (Bethesda, Md.) · 2022Article
- Methodologies for theGenes · 2022Review
- Small RNA pathways in the nematode Ascaris in the absence of piRNAs.Nature communications · 2022Article
- msRepDB: a comprehensive repetitive sequence database of over 80 000 species.Nucleic acids research · 2022Article
- Finding and Characterizing Repeats in Plant Genomes.Methods in molecular biology (Clifton, N.J.) · 2022Article
- Comparative genomic and transcriptomic analyses of transposable elements in polychaetous annelids highlight LTR retrotransposon diversity and evolution.Mobile DNA · 2021Article
- A sensitive repeat identification framework based on short and long reads.Nucleic acids research · 2021Article
- Genomics and transcriptomics of epizoic Seisonidea (Rotifera, syn. Syndermata) reveal strain formation and gradual gene loss with growing ties to the host.BMC genomics · 2021Article
- Review
- Global analysis of repetitive DNA from unassembled sequence reads using RepeatExplorer2.Nature protocols · 2020Article
- RepAHR: an improved approach for de novo repeat identification by assembly of the high-frequency reads.BMC bioinformatics · 2020Article
- The Drosophila Y Chromosome Affects Heterochromatin Integrity Genome-Wide.Molecular biology and evolution · 2020Article
- The Y chromosome may contribute to sex-specific ageing in Drosophila.Nature ecology & evolution · 2020Article
- Seq'ing identity and function in a repeat-derived noncoding RNA world.Chromosome research : an international journal on the molecular, supramolecular and evolutionary aspects of chromosome biology · 2020Review
- A new statistic for efficient detection of repetitive sequences.Bioinformatics (Oxford, England) · 2019Article
- DeviaTE: Assembly-free analysis and visualization of mobile genetic element composition.Molecular ecology resources · 2019Article
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3 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Generation of repeat libraries is a critical step for analysis of complex genomes. In the era of next-generation sequencing (NGS), such libraries are usually produced using a whole-genome shotgun (WGS) derived reference sequence whose completeness greatly influences the quality of derived repeat libraries. We describe here a de novo repeat assembly method--RepARK (Repetitive motif detection by Assembly of Repetitive K-mers)--which avoids potential biases by using abundant k-mers of NGS WGS reads without requiring a reference genome. For validation, repeat consensuses derived from simulated and real Drosophila melanogaster NGS WGS reads were compared to repeat libraries generated by four established methods. RepARK is orders of magnitude faster than the other methods and generates libraries that are: (i) composed almost entirely of repetitive motifs, (ii) more comprehensive and (iii) almost completely annotated by TEclass. Additionally, we show that the RepARK method is applicable to complex genomes like human and can even serve as a diagnostic tool to identify repetitive sequences contaminating NGS datasets.
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