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

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.