ArticleGigaScience2020
TRiCoLOR: tandem repeat profiling using whole-genome long-read sequencing data.
Article in GigaScience, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 22 papers, 1 of them a synthesis that pooled it.
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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.
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Who cites it
22 citing papers in PubMed, 1 synthesis or guideline pooled it, 28 citations in OpenAlex.
- A practical guide to identifying associations between tandem repeats and complex human traits using consensus genotypes from multiple tools.Nature protocols · 2026Guideline
- Toward the clinical application of long-read sequencing in repeat-expansion disorders.Nature genetics · 2026Review
- Detection of short tandem repeats in the cattle genome: a comparison of bioinformatic tools.BMC genomics · 2026Article
- Computational tools for tandem repeat detection using long-read sequencing.Briefings in bioinformatics · 2026Review
- The continued promise of genomic technologies and software in neurogenetics.Journal of neuromuscular diseases · 2025Review
- TRsv: simultaneous detection of tandem repeat variations, structural variations, and short indels using long read sequencing data.Genome biology · 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
- Fusarium Genome Sequencing and Assembly.Methods in molecular biology (Clifton, N.J.) · 2025Article
- LongTR: genome-wide profiling of genetic variation at tandem repeats from long reads.Genome biology · 2024Article
- Sequencing and characterizing short tandem repeats in the human genome.Nature reviews. Genetics · 2024Review
- Expanding horizons of tandem repeats in biology and medicine: Why 'genomic dark matter' matters.Emerging topics in life sciences · 2023Article
- Evolutionary Study of Protein Short Tandem Repeats in Protein Families.Biomolecules · 2023Article
- NanoSTR: A method for detection of target short tandem repeats based on nanopore sequencing data.Frontiers in molecular biosciences · 2023Article
- DeepRepeat: direct quantification of short tandem repeats on signal data from nanopore sequencing.Genome biology · 2022Article
- The third international hackathon for applying insights into large-scale genomic composition to use cases in a wide range of organisms.F1000Research · 2022Article
- Nanopore sequencing technology, bioinformatics and applications.Nature biotechnology · 2021Review
- Review
- Towards population-scale long-read sequencing.Nature reviews. Genetics · 2021Review
- CaBagE: A Cas9-based Background Elimination strategy for targeted, long-read DNA sequencing.PloS one · 2021Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
5 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundTandem repeat sequences are widespread in the human genome, and their expansions cause multiple repeat-mediated disorders. Genome-wide discovery approaches are needed to fully elucidate their roles in health and disease, but resolving tandem repeat variation accurately remains a challenging task. While traditional mapping-based approaches using short-read data have severe limitations in the size and type of tandem repeats they can resolve, recent third-generation sequencing technologies exhibit substantially higher sequencing error rates, which complicates repeat resolution.
resultsWe developed TRiCoLOR, a freely available tool for tandem repeat profiling using error-prone long reads from third-generation sequencing technologies. The method can identify repetitive regions in sequencing data without a prior knowledge of their motifs or locations and resolve repeat multiplicity and period size in a haplotype-specific manner. The tool includes methods to interactively visualize the identified repeats and to trace their Mendelian consistency in pedigrees.
conclusionsTRiCoLOR demonstrates excellent performance and improved sensitivity and specificity compared with alternative tools on synthetic data. For real human whole-genome sequencing data, TRiCoLOR achieves high validation rates, suggesting its suitability to identify tandem repeat variation in personal genomes.
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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.