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Updated: Apr 29, 2026

Sequencing of mRNA from Whole Blood using Nanopore Sequencing

Sequencing of mRNA from Whole Blood using Nanopore Sequencing

Published on: June 3, 2019

Telomere-to-telomere assembly using HERRO-corrected Nanopore Simplex reads.

Dominik Stanojević^1,2, Dehui Lin¹, Sergey Nurk³

¹Laboratory of AI in Genomics, Genome Institute of Singapore, A*STAR, Singapore, Singapore.

|April 27, 2026

Summary

This summary is machine-generated.

A new deep learning method, HERRO, corrects ultra-long Oxford Nanopore Simplex reads, enabling high-quality telomere-to-telomere genome assemblies. This approach reduces costs and improves genomic analysis by using error-corrected reads.

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Last Updated: Apr 29, 2026

Sequencing of mRNA from Whole Blood using Nanopore Sequencing

Sequencing of mRNA from Whole Blood using Nanopore Sequencing

Published on: June 3, 2019

Ultra-long Read Sequencing for Whole Genomic DNA Analysis

Ultra-long Read Sequencing for Whole Genomic DNA Analysis

Published on: March 15, 2019

Rare Event Detection Using Error-corrected DNA and RNA Sequencing

Rare Event Detection Using Error-corrected DNA and RNA Sequencing

Published on: August 3, 2018

Area of Science:

Genomics
Bioinformatics
Computational Biology

Background:

Telomere-to-telomere (T2T) phased assemblies are the gold standard for reference genomes but are costly and complex.
Current T2T assembly methods often require multiple sequencing platforms and large DNA inputs.
High-accuracy long reads (e.g., PacBio HiFi) and ultra-long reads (ONT Simplex) are typically combined.

Purpose of the Study:

To demonstrate that high-quality T2T genome assemblies can be achieved using only error-corrected ultra-long Oxford Nanopore (ONT) Simplex reads.
To introduce HERRO, a deep learning framework for haplotype-aware error correction of ONT Simplex reads.
To reduce the cost and complexity of generating reference-quality genome assemblies.

Main Methods:

Development of the HERRO (Haplotype-aware ERRor cOrrection) deep learning framework.
Correction of ultra-long ONT Simplex reads, preserving haplotype-specific differences.
Assembly of corrected reads using the Verkko assembler.

Main Results:

HERRO increased read accuracy up to 100-fold for diploid human genomes.
T2T assemblies of up to 32 chromosomes, including sex chromosomes, were reconstructed.
Consistent NGA50 values of >= 100 Mb were achieved across multiple human genomes.
The method supports R9.4.1 and R10.4.1 ONT Simplex reads and generalizes to other species.

Conclusions:

Error-corrected ONT Simplex reads can generate high-quality T2T genome assemblies.
The HERRO framework significantly improves read accuracy while preserving haplotype information.
This approach offers a cost-effective and efficient alternative for high-quality genome sequencing and analysis.