ArticleGenome biology2022
DeepRepeat: direct quantification of short tandem repeats on signal data from nanopore sequencing.
Article in Genome biology, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 35 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
35 citing papers in PubMed.
- Somatic mosaicism in the brain: linking development, ageing and neurodegeneration.Nature reviews. Neurology · 2026Review
- Toward the clinical application of long-read sequencing in repeat-expansion disorders.Nature genetics · 2026Review
- Optimized Cas9-Enriched Nanopore Sequencing and Analysis Workflow for Clinical Diagnosis of Repeat Expansion Disorders.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Article
- Large-scale human genomic resources drive innovations toward forensic intelligent source attribution and precision identification.International journal of legal medicine · 2026Review
- Quantification of disease-associated RNA tandem repeats by nanopore sensing.Nature communications · 2026Article
- Targeted long-read sequencing for high-resolution repeat profiling in myotonic dystrophy type 1.Experimental & molecular medicine · 2026Article
- Computational tools for tandem repeat detection using long-read sequencing.Briefings in bioinformatics · 2026Review
- Development of a Multiplex Amplification System Using Oxford Nanopore Sequencing for STRs and InDels.Human mutation · 2026Article
- The continued promise of genomic technologies and software in neurogenetics.Journal of neuromuscular diseases · 2025Review
- Association of human-specific expanded short tandem repeats with neuron-specific regulatory features.Science advances · 2025Article
- A Hitchhiker's Guide to long-read genomic analysis.Genome research · 2025Review
- Review
- A detailed analysis of second and third-generation sequencing approaches for accurate length determination of short tandem repeats and homopolymers.Nucleic acids research · 2025Article
- Enhanced detection and genotyping of disease-associated tandem repeats using HMMSTR and targeted long-read sequencing.Nucleic acids research · 2025Article
- Navigating triplet repeats sequencing: concepts, methodological challenges and perspective for Huntington's disease.Nucleic acids research · 2025Review
- NanoMnT: an STR analysis tool for Oxford Nanopore sequencing data driven by a comprehensive analysis of error profile in STR regions.GigaScience · 2025Article
- Next-generation sequencing-based tools or nanopore-based tools: which is more suitable for short tandem repeats genotyping of nanopore sequencing?Bioinformatics advances · 2025Article
- Comprehensive identification of pathogenic tandem repeat expansions in sporadic amyotrophic lateral sclerosis: advantages of long-read vs. short-read sequencing.Experimental biology and medicine (Maywood, N.J.) · 2025Article
- Get ready for short tandem repeats analysis using long reads-the challenges and the state of the art.Frontiers in genetics · 2025Review
- LongReadSum: A fast and flexible quality control and signal summarization tool for long-read sequencing data.Computational and structural biotechnology journal · 2025Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
6 authors.
Funding
Abstract
Despite recent improvements in basecalling accuracy, nanopore sequencing still has higher error rates on short-tandem repeats (STRs). Instead of using basecalled reads, we developed DeepRepeat which converts ionic current signals into red-green-blue channels, thus transforming the repeat detection problem into an image recognition problem. DeepRepeat identifies and accurately quantifies telomeric repeats in the CHM13 cell line and achieves higher accuracy in quantifying repeats in long STRs than competing methods. We also evaluate DeepRepeat on genome-wide or candidate region datasets from seven different sources. In summary, DeepRepeat enables accurate quantification of long STRs and complements existing methods relying on basecalled reads.
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.