• NextPolish2 is a repeat-aware polishing tool specifically designed for genomes assembled from HiFi long reads, addressing base errors without overcorrection.
• It incorporates a built-in phasing module that maintains haplotype consistency and reduces switch errors in heterozygous regions.
• The tool outperforms the Racon + Merfin pipeline in polishing the human T2T genome assembly, improving accuracy in highly repetitive regions.
• NextPolish2 is freely available as open-source software, facilitating its adoption for T2T genome projects.