Centromere and Satellite Annotation

This repository hosts a comprehensive data and workflow resource for Centromere and Satellite Annotation in the APGp1 genome assembly.

---

1. Overview

This project provides precise characterization of centromeric regions, including:

• Complete Centromere Coordinates
• Detailed Satellite and Higher-Order Repeat (HOR) Annotation Tracks
• Robust Pipelines for HOR identification and Satellite Annotation.

---

2. Data Access

The Annotation directory contains the final, high-quality annotation data.

• Complete centromere coordinates in APGp1 : APGp1_complete_centromere

• Satellite tracks for each phased assembly: native_bed_format

• HOR identified by HORmon: HOR_HORmon

• HOR identified by HiCAT: HOR_HiCAT

• CENP-A enrichment boundaries: native_bed_format

The Results directory contains analysis outputs and supplementary data files.

• Centromere architecture figures (PDF): Centromere_Architecture_Figures.zip

• CenHap classification table (TXT): CenHap_Classification_Table.txt

• CENP-A CDR images (PDF): CENPA_CDR_Images.zip

• Pericentromeric phylogeny & tanglegrams (PDF, Newick): Pericentromeric_Phylogeny_and_Tanglegrams.zip

• Mutation sample pairs (PDF): Mutation_Sample_Pairs.zip

3. Recommended Workflows

We provide and highly recommend the following two pipelines for future T2T human assemblies and related satellite studies.

SatelliteAnnotationWorkflow

Directory: SatelliteAnnotationWorkflow

This workflow was developed for the comprehensive annotation of centromeric satellites (including $\alpha$, $\beta$, $\gamma$, HSat1, HSat2, and HSat3) in human assemblies. The pipeline outputs precise centromeric coordinates for each genome and provides scripts for result visualization.

• Access Workflow

HORmining Pipeline

Directory: HORmining

HORmining is a bioinformatics pipeline designed for robust identification of Higher-Order Repeat (HOR) structures within alpha satellite DNA. It integrates two complementary computational approaches: the graph-based HORmon algorithm and the hierarchical tandem repeat mining (HTRM)-based HiCAT algorithm.

• Access Workflow

---

4. Integrated Analysis (Code Archive)

The Analysis directory contains the source code used for the final, integrated analysis of global centromere diversity, structural characterization, and evolutionary comparisons.