ArticlePloS one2016
REPdenovo: Inferring De Novo Repeat Motifs from Short Sequence Reads.
Article in PloS one, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 33 papers.
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Who cites it
33 citing papers in PubMed.
- Detection of short tandem repeats in the cattle genome: a comparison of bioinformatic tools.BMC genomics · 2026Article
- A draft genome assembly for the dart-poison frogGigaByte (Hong Kong, China) · 2025Article
- Study of Dispersed Repeats in theInternational journal of molecular sciences · 2024Article
- Centuries of genome instability and evolution in soft-shell clam, Mya arenaria, bivalve transmissible neoplasia.Nature cancer · 2023Article
- Repetitive DNA sequence detection and its role in the human genome.Communications biology · 2023Review
- Genome assembly composition of the String "ACGT" array: a review of data structure accuracy and performance challenges.PeerJ. Computer science · 2023Article
- Twinkle twinkle brittle star: the draft genome of Ophioderma brevispinum (Echinodermata: Ophiuroidea) as a resource for regeneration research.BMC genomics · 2022Article
- Methodologies for theGenes · 2022Review
- msRepDB: a comprehensive repetitive sequence database of over 80 000 species.Nucleic acids research · 2022Article
- A dense linkage map for a large repetitive genome: discovery of the sex-determining region in hybridizing fire-bellied toads (Bombina bombina and Bombina variegata).G3 (Bethesda, Md.) · 2021Article
- A sensitive repeat identification framework based on short and long reads.Nucleic acids research · 2021Article
- Review
- Gene family amplification facilitates adaptation in freshwater unionid bivalve Megalonaias nervosa.Molecular ecology · 2021Article
- BigFiRSt: A Software Program Using Big Data Technique for Mining Simple Sequence Repeats From Large-Scale Sequencing Data.Frontiers in big data · 2021Article
- 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
- Chromosome-Level Assembly ofG3 (Bethesda, Md.) · 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
- Sequencing and Functional Annotation of the Whole Genome ofG3 (Bethesda, Md.) · 2020Article
- TheFrontiers in genetics · 2020Article
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Authors and funding
3 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Repeat elements are important components of eukaryotic genomes. One limitation in our understanding of repeat elements is that most analyses rely on reference genomes that are incomplete and often contain missing data in highly repetitive regions that are difficult to assemble. To overcome this problem we develop a new method, REPdenovo, which assembles repeat sequences directly from raw shotgun sequencing data. REPdenovo can construct various types of repeats that are highly repetitive and have low sequence divergence within copies. We show that REPdenovo is substantially better than existing methods both in terms of the number and the completeness of the repeat sequences that it recovers. The key advantage of REPdenovo is that it can reconstruct long repeats from sequence reads. We apply the method to human data and discover a number of potentially new repeats sequences that have been missed by previous repeat annotations. Many of these sequences are incorporated into various parasite genomes, possibly because the filtering process for host DNA involved in the sequencing of the parasite genomes failed to exclude the host derived repeat sequences. REPdenovo is a new powerful computational tool for annotating genomes and for addressing questions regarding the evolution of repeat families. The software tool, REPdenovo, is available for download at https://github.com/Reedwarbler/REPdenovo.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.