ArticleGenome biology2023
HiCAT: a tool for automatic annotation of centromere structure.
Article in Genome biology, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 32 papers.
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Who cites it
32 citing papers in PubMed.
- Fusion-Derived Centromeres Reveal Satellite Repeat Remodeling inPlants (Basel, Switzerland) · 2026Article
- EasyCen: A Lightweight Framework for Centromere Localisation and Repeat-Organisation Profiling in Telomere-to-Telomere Genomes.Molecular ecology resources · 2026Article
- Enabling efficient and robust analysis of tandem repeats in genomic data using Wavefront-based String Decomposer.Genome research · 2026Article
- Rapid centromere turnover and the adaptive radiation of lemurs.bioRxiv : the preprint server for biology · 2026Article
- Article
- Higher order repeat structures reflect diverging evolutionary paths in maize centromeres and knobs.Genome biology · 2026Article
- Haplotype-resolved and near telomere-to-telomere assembly of the autotetraploid potato genome.Genome biology · 2026Article
- The near-complete genome assembly of allotetraploidHorticulture research · 2026Article
- Analysis of a near telomere-to-telomere genome of Phellodendron amurense reveals insights into berberine biosynthesis.Nature communications · 2025Article
- Hybridization Drives Trait Integration in Telomere-To-Telomere Apocynum Genomes.Plant biotechnology journal · 2025Article
- RepeatOBserver: Tandem Repeat Visualisation and Putative Centromere Detection.Molecular ecology resources · 2025Article
- Article
- Genetic Analysis of Lodging Resistance in 1892S Based on the T2T Genome: Providing a Genetic Approach for the Improvement of Two-Line Hybrid Rice Varieties.Plants (Basel, Switzerland) · 2025Article
- Long and Accurate: How HiFi Sequencing is Transforming Genomics.Genomics, proteomics & bioinformatics · 2025Review
- Fast sequence alignment for centromeres with RaMA.Genome research · 2025Article
- Post-polyploidization centromere evolution in cotton.Nature genetics · 2025Article
- A Near Complete Genome Assembly of the Oshima Cherry Cerasus speciosa.Scientific data · 2025Article
- Centromere Landscapes Resolved from Hundreds of Human Genomes.Genomics, proteomics & bioinformatics · 2024Article
- Long-read de novo genome assembly of Gulf toadfish (Opsanus beta).BMC genomics · 2024Article
- The centromere landscapes of four karyotypically diverse Papaver species provide insights into chromosome evolution and speciation.Cell genomics · 2024Article
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Authors and funding
6 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Significant improvements in long-read sequencing technologies have unlocked complex genomic areas, such as centromeres, in the genome and introduced the centromere annotation problem. Currently, centromeres are annotated in a semi-manual way. Here, we propose HiCAT, a generalizable automatic centromere annotation tool, based on hierarchical tandem repeat mining to facilitate decoding of centromere architecture. We apply HiCAT to simulated datasets, human CHM13-T2T and gapless Arabidopsis thaliana genomes. Our results are generally consistent with previous inferences but also greatly improve annotation continuity and reveal additional fine structures, demonstrating HiCAT's performance and general applicability.
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