ArticleBioinformatics (Oxford, England)2019
TideHunter: efficient and sensitive tandem repeat detection from noisy long-reads using seed-and-chain.
Article in Bioinformatics (Oxford, England), 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 37 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
37 citing papers in PubMed.
- AniAnn's: alignment-free annotation of tandem repeat arrays using fast average nucleotide identity estimates.Bioinformatics (Oxford, England) · 2026Article
- The ageing holobiont: crosstalk between telomere dynamics, oxidative stress and the gut microbiome.Biological reviews of the Cambridge Philosophical Society · 2026Review
- Genome evolution in parthenogenetic nematodes shaped by chromosome rearrangements and introgression.Genome research · 2026Article
- A new genome assembly of the pea cultivar 'Caméor' provides resources for functional genomics and genetics.Scientific data · 2026Article
- Integrative satellitomics reveals distinct patterns of organization, transcription and evolution of satellite DNAs in Tenebrio molitor.Biology direct · 2026Article
- Mixed modes of satellite DNA and transposable element evolution, which shape the repetitive landscape of air-breathing catfishes (Clarias).Chromosome research : an international journal on the molecular, supramolecular and evolutionary aspects of chromosome biology · 2026Article
- Allelic variation at a single locus distinguishes spring and winter faba beans.Nature genetics · 2026Article
- ECCFP: A consecutive full pass-based bioinformatic analysis for eccDNA identification from long-read sequencing data.iMetaOmics · 2026Article
- Divergence and conservation of satellite DNA in the loggerhead sea turtle (Caretta caretta): a comparative cytogenomic analysis.Chromosome research : an international journal on the molecular, supramolecular and evolutionary aspects of chromosome biology · 2026Article
- Sequencing complete plasmids on Oxford Nanopore Technologies sequencers using R2C2 and Chopper.PloS one · 2026Article
- Rebalancing the seed proteome following deletion of vicilin-related genes in pea (Pisum sativum L.).Journal of experimental botany · 2025Article
- Oxford nanopore sequencing as a useful tool for investigating the population dynamics of invasive begomoviruses in Sicily.Microbial genomics · 2025Article
- Article
- RepeatOBserver: Tandem Repeat Visualisation and Putative Centromere Detection.Molecular ecology resources · 2025Article
- TeloSearchLR: an algorithm to detect novel telomere repeat motifs using long sequencing reads.G3 (Bethesda, Md.) · 2025Article
- Circular RNA discovery with emerging sequencing and deep learning technologies.Nature genetics · 2025Review
- A method for in-depth analysis of circular DNA virus populations by unambiguously profiling the low abundant virus variants and partial genomic components.Nucleic acids research · 2025Article
- Improvement of Nanopore sequencing provides access to high quality genomic data for multi-component CRESS-DNA plant viruses.Virology journal · 2025Article
- A chromosome-scale reference genome of grasspea (Lathyrus sativus).Scientific data · 2024Article
- Comparative genomics illuminates karyotype and sex chromosome evolution of sharks.Cell genomics · 2024Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
4 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
motivationPacific Biosciences (PacBio) and Oxford Nanopore Technologies (ONT) sequencing technologies can produce long-reads up to tens of kilobases, but with high error rates. In order to reduce sequencing error, Rolling Circle Amplification (RCA) has been used to improve library preparation by amplifying circularized template molecules. Linear products of the RCA contain multiple tandem copies of the template molecule. By integrating additional in silico processing steps, these tandem sequences can be collapsed into a consensus sequence with a higher accuracy than the original raw reads. Existing pipelines using alignment-based methods to discover the tandem repeat patterns from the long-reads are either inefficient or lack sensitivity.
resultsWe present a novel tandem repeat detection and consensus calling tool, TideHunter, to efficiently discover tandem repeat patterns and generate high-quality consensus sequences from amplified tandemly repeated long-read sequencing data. TideHunter works with noisy long-reads (PacBio and ONT) at error rates of up to 20% and does not have any limitation of the maximal repeat pattern size. We benchmarked TideHunter using simulated and real datasets with varying error rates and repeat pattern sizes. TideHunter is tens of times faster than state-of-the-art methods and has a higher sensitivity and accuracy. AVAILABILITY AND IMPLEMENTATION: TideHunter is written in C, it is open source and is available at https://github.com/yangao07/TideHunter.
Indexed as
Identifiers
What OpenQuestion holds
Registered trials
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.