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Genome Annotation and Assembly

Genome Annotation and Assembly

The genome refers to all of the genetic material in an organism. It can range from a few million base pairs in microbial cells to several billion base pairs in many eukaryotic organisms. Genome assembly refers to the process of taking the DNA sequencing data and putting it all back together in a correct order to create a close representation of the original genome. This is followed by the identification of functional elements on the newly assembled genome, a process called genome annotation.

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Updated: Jun 24, 2025

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NextPolish2: A Repeat-aware Polishing Tool for Genomes Assembled Using HiFi Long Reads.

Jiang Hu^1,2, Zhuo Wang², Fan Liang²

¹School of Automation Science and Engineering, Faculty of Electronic and Information Engineering, Xi'an Jiaotong University, Xi'an 710049, China.

Genomics, Proteomics & Bioinformatics

|June 11, 2024

Summary

NextPolish2 refines genome assemblies from PacBio HiFi long reads, fixing base errors without introducing overcorrections or haplotype switches. This tool enhances the accuracy of telomere-to-telomere genomes.

Keywords:

Error correction Genome assembly Genome polishing HiFi long read Telomere-to-telomere

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Area of Science:

Genomics
Bioinformatics
Molecular Biology

Background:

PacBio's high-fidelity (HiFi) long-read sequencing advances genome assembly accuracy.
HiFi reads still contain base-level errors, especially in error-prone regions.
Current genome polishing tools often cause overcorrections and haplotype switch errors.

Purpose of the Study:

To introduce NextPolish2, an upgraded genome polishing tool.
To address limitations of existing tools in correcting HiFi long-read assemblies.
To improve the accuracy of telomere-to-telotone (T2T) genomes.

Main Methods:

Development of NextPolish2, an enhanced genome polishing algorithm.
Application of NextPolish2 to correct base errors in HiFi long-read genome assemblies.
Evaluation of NextPolish2's performance in minimizing overcorrections and haplotype switch errors.

Main Results:

NextPolish2 effectively corrects base errors in HiFi genome assemblies.
The tool avoids introducing excessive overcorrections.
NextPolish2 minimizes haplotype switch errors during the polishing process.

Conclusions:

NextPolish2 offers a significant improvement for polishing HiFi long-read genome assemblies.
The tool is crucial for enhancing the accuracy of T2T genomes.
NextPolish2 is freely available, promoting its adoption in genomic research.