ArticleGenomics, proteomics & bioinformatics2024
NextPolish2: A Repeat-aware Polishing Tool for Genomes Assembled Using HiFi Long Reads.
Article in Genomics, proteomics & bioinformatics, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 81 papers.
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81 citing papers in PubMed.
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- The telomere-to-telomere gap-free reference genome and DNA methylome unveil epigenetic regulation of proanthocyanidin biosynthesis during apricot fruit development.The Plant journal : for cell and molecular biology · 2026Article
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- Near telomere-to-telomere genome assembly of the rainbow trout (Oncorhynchus mykiss).Scientific data · 2026Article
- Haplotype-resolved T2T genome and population resequencing provide insights into the domestication and mogroside biosynthesis ofHorticulture research · 2026Article
- Chromosome-level genome assembly of the jumping spider Spartaeus platnicki.Scientific data · 2026Article
- A chromosome-level reference genome assembly and annotation of Serrodes campana.Scientific data · 2026Article
- From contiguity to accuracy: Validation-centered perspectives on bacterial genome assembly.Journal of microbiology (Seoul, Korea) · 2026Review
- A Near Telomere-to-Telomere Genome of Belamcanda chinensis Provides Insights Into Genome Evolution and the Biosynthesis of Characteristic Isoflavones.Plant biotechnology journal · 2026Article
- Characterization of the mitochondrial genome of the aquatic vegetable Eleocharis dulcis (Burm. f.) Trin. ex Hensch.: the first representative of genus Eleocharis with evolutionary insights in Cyperaceae.BMC plant biology · 2026Article
- A haplotype-resolved nutmeg genome reveals XY sex chromosome evolution and enables molecular sexing.Communications biology · 2026Article
- Haplotype-resolved chromosome-level genome assemblies of the deep-sea annelid Lindaspio polybranchiata.Scientific data · 2026Article
- Haplotype-resolved telomere-to-telomere assembly and haplotype-aware annotation pipeline enable high-quality reannotation of threeHorticulture research · 2026Article
- Near complete telomere-to-telomere level genome assembly of blackchin tilapia (Sarotherodon melanotheron).Scientific data · 2026Article
- MarpolBase: genome database for Marchantia polymorpha featuring high quality reference genome sequences.Plant & cell physiology · 2026Article
- Telomere-to-Telomere gap-free genome assembly of the allotetraploid wild raspberry Rubus alceifolius Poir.Scientific data · 2026Article
- Chromosome-Level Genome Assembly and Annotation of Piptanthus nepalensis (Hook.) Sweet.Scientific data · 2026Article
- High-quality genome ofPlant diversity · 2026Article
21 more citing papers are in PubMed but not listed here.
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Authors and funding
6 authors.
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No grant is acknowledged in the PubMed record.
Abstract
The high-fidelity (HiFi) long-read sequencing technology developed by PacBio has greatly improved the base-level accuracy of genome assemblies. However, these assemblies still contain base-level errors, particularly within the error-prone regions of HiFi long reads. Existing genome polishing tools usually introduce overcorrections and haplotype switch errors when correcting errors in genomes assembled from HiFi long reads. Here, we describe an upgraded genome polishing tool - NextPolish2, which can fix base errors remaining in those "highly accurate" genomes assembled from HiFi long reads without introducing excessive overcorrections and haplotype switch errors. We believe that NextPolish2 has a great significance to further improve the accuracy of telomere-to-telomere (T2T) genomes. NextPolish2 is freely available at https://github.com/Nextomics/NextPolish2.
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