quarTeT

quartet: Toolkit for Telomere-to-Telomere Genome Assembly and Chromosome Feature Analysis

quartet performs telomere-to-telomere (T2T) genome assembly and structural characterization by organizing phased contigs into chromosome-level assemblies, closing assembly gaps with ultra-long sequences, and identifying telomeric and centromeric regions.

Key Features:

• AssemblyMapper: Assembles phased contigs into chromosome-level genomes using closely related reference genomes.
• GapFiller: Closes unfilled assembly gaps by integrating additional ultra-long sequences to improve genome completeness.
• TeloExplorer: Detects candidate telomeres and determines their chromosomal localization.
• CentroMiner: Identifies and maps centromeric regions within assembled genomes.
• Modular Architecture: Enables independent or combined use of AssemblyMapper, GapFiller, TeloExplorer, and CentroMiner.

Scientific Applications:

• Telomere-to-Telomere Genome Assembly: Generates high-quality chromosome-level assemblies, including the Actinidia chinensis genome comparable to Hongyang v4.0.
• Centromere Identification: Detects centromeric regions in model organisms such as Arabidopsis thaliana and Oryza sativa, consistent with experimental validation.

Methodology:

AssemblyMapper orders and orients phased contigs against closely related reference genomes to construct chromosome-level assemblies. GapFiller integrates ultra-long sequencing reads to bridge unresolved gaps. TeloExplorer identifies telomeric repeat candidates and localizes them to chromosome termini. CentroMiner detects centromeric regions and maps their genomic positions for structural characterization.