Yibin Wang

Genetic Architecture of Sugarcane Traits in a Polyploid Genomics Framework

Wed, 27 May 2026 00:00:00 +0000

The Haplotype-Resolved and near-Telomere-to-Telomere Genome Assembly for the Autotetraploid Alfalfa

Thu, 01 Jan 2026 00:00:00 +0000

MIKE: An Ultrafast, Assembly-, and Alignment-Free Approach for Phylogenetic Tree Construction

Mon, 01 Apr 2024 00:00:00 +0000

A Chromosomal-Scale Genome Assembly of Modern Cultivated Hybrid Sugarcane Provides Insights into Origination and Evolution

Mon, 01 Jan 2024 00:00:00 +0000

Chromosome-Level Scaffolding of Haplotype-Resolved Assemblies Using Hi-C Data without Reference Genomes

Mon, 01 Jan 2024 00:00:00 +0000

JCVI: A Versatile Toolkit for Comparative Genomics Analysis

Mon, 01 Jan 2024 00:00:00 +0000

Recent Advances in Assembly of Plant Complex Genomes

Sat, 01 Apr 2023 00:00:00 +0000

Gene Mining and Genomics-Assisted Breeding Empowered by the Pangenome of Tea Plant Camellia Sinensis

Sun, 01 Jan 2023 00:00:00 +0000

Sequencing and Assembly of Polyploid Genomes

Sun, 01 Jan 2023 00:00:00 +0000

Genomic Insights into the Recent Chromosome Reduction of Autopolyploid Sugarcane Saccharum Spontaneum

Sat, 01 Jan 2022 00:00:00 +0000

Haplotype-Resolved Genome Assembly Provides Insights into Evolutionary History of the Tea Plant Camellia Sinensis

Fri, 01 Jan 2021 00:00:00 +0000

Genomes of the Banyan Tree and Pollinator Wasp Provide Insights into Fig-Wasp Coevolution

Sun, 01 Nov 2020 00:00:00 +0000

Unzipping Haplotypes in Diploid and Polyploid Genomes

Wed, 01 Jan 2020 00:00:00 +0000

C-Phasing

Mon, 01 Jan 0001 00:00:00 +0000

Overview

C-Phasing is an open-source framework for chromosome-scale, haplotype-resolved assembly of polyploid genomes. It integrates long-read sequencing, Hi-C and Pore-C chromatin interaction data to accurately reconstruct homologous chromosomes in complex genomes with high ploidy and low sequence divergence.

Designed for modern polyploid genome projects, C-Phasing provides an end-to-end solution from chromosome partitioning to scaffolding while remaining compatible with both conventional Hi-C and long-read Pore-C technologies.

Key Features

Hypergraph-based chromosome partitioning using multi-way chromatin interactions
Support for both Hi-C and Pore-C data
Methylation-assisted alignment refinement (MethAlign)
Chimeric contig detection (Hitig)
Copy-number-aware collapsed contig rescue (CollapseRescue)
Chromosome-scale scaffolding for complex polyploid genomes

Applications

C-Phasing has been evaluated across a diverse collection of polyploid genomes, including potato, sweet potato, alfalfa, sugarcane and other complex plant genomes, consistently improving chromosome completeness, haplotype resolution and structural accuracy.

Resources

Source code:
Documentation:
Manuscript: (under submit)

Contact

Mon, 01 Jan 0001 00:00:00 +0000

Email:
GitHub:
Google Scholar:
ORCID: