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Related Experiment Video

Updated: Dec 6, 2025

Ultra-long Read Sequencing for Whole Genomic DNA Analysis
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TRiCoLOR: tandem repeat profiling using whole-genome long-read sequencing data.

Davide Bolognini1,2, Alberto Magi3, Vladimir Benes2

  • 1Department of Experimental and Clinical Medicine, University of Florence, Viale Pieraccini 6, Florence 50134, Italy.

Gigascience
|October 9, 2020
PubMed
Summary
This summary is machine-generated.

TRiCoLOR accurately profiles tandem repeats using long-read sequencing, overcoming challenges posed by high error rates. This tool aids in understanding repeat variations in the human genome and their links to disease.

Keywords:
bioinformatics softwarelong-read sequencingtandem repeat variation

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Area of Science:

  • Genomics
  • Bioinformatics
  • Molecular Biology

Background:

  • Tandem repeat sequences are prevalent in the human genome and linked to various disorders when expanded.
  • Accurate genome-wide discovery of tandem repeat variation is crucial for understanding health and disease.
  • Short-read sequencing has limitations in resolving tandem repeats, while third-generation sequencing's error rates pose challenges.

Purpose of the Study:

  • To develop a tool for accurate tandem repeat profiling using long-read sequencing data.
  • To address the challenges of repeat resolution in the presence of high sequencing error rates.
  • To enable haplotype-specific analysis of repeat multiplicity and period size.

Main Methods:

  • Development of TRiCoLOR, a tool for tandem repeat profiling.
  • Utilizes error-prone long reads from third-generation sequencing technologies.
  • Includes methods for interactive visualization and Mendelian consistency tracing.

Main Results:

  • TRiCoLOR identifies repetitive regions without prior motif or location knowledge.
  • The tool resolves repeat multiplicity and period size in a haplotype-specific manner.
  • Demonstrates superior performance, sensitivity, and specificity compared to alternative tools on synthetic data.

Conclusions:

  • TRiCoLOR achieves high validation rates on real human whole-genome sequencing data.
  • The tool is suitable for identifying tandem repeat variation in personal genomes.
  • Facilitates a deeper understanding of the role of tandem repeats in human health and disease.