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Updated: Aug 22, 2025

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Duet: SNP-assisted structural variant calling and phasing using Oxford nanopore sequencing.

Yekai Zhou1, Amy Wing-Sze Leung1, Syed Shakeel Ahmed1

  • 1Department of Computer Science, The University of Hong Kong, Hong Kong, China.

BMC Bioinformatics
|November 7, 2022
PubMed
Summary

Duet accurately calls and phases structural variants (SVs) using Oxford Nanopore Technologies (ONT) long-read sequencing data. This tool excels even at low sequencing coverage, offering improved performance for clinical applications.

Keywords:
Oxford Nanopore SequencingSNP callingSV genotypingSV phasingStructural variant (SV) calling

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Area of Science:

  • Genomics
  • Bioinformatics

Background:

  • Long-read sequencing with Oxford Nanopore Technologies (ONT) MinION offers cost-effective whole genome sequencing for structural variant (SV) detection.
  • Accurate SV calling and phasing remain challenging despite the advantages of long reads.

Purpose of the Study:

  • To introduce Duet, a novel tool for optimized SV detection, calling, and phasing using ONT data.
  • To evaluate Duet's performance against state-of-the-art tools across various sequencing coverages.

Main Methods:

  • Duet integrates novel features from both SV and single-nucleotide polymorphism (SNP) signatures.
  • Benchmarking was performed on multiple ONT sequencing datasets with coverages from 8× to 40×.

Main Results:

  • Duet demonstrated superior performance in SV calling, genotyping, and phasing at low sequencing coverage (8×).
  • At higher coverages (20×–40×), Duet maintained high performance in SV calling and genotyping, with further improvements in SV phasing F1-score.

Conclusions:

  • Duet accurately performs SV calling, genotyping, and phasing, particularly with low-coverage ONT data, making it valuable for low-coverage genomes.
  • The tool shows excellent scalability and adaptability for diverse clinical applications with high-coverage genomes.