C-Phasing

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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

Computational Genomics Polyploid Genome Assembly Pore-C Hi-C Rust
Yibin Wang
Authors
Yibin Wang
PhD Candidate
I am a PhD candidate at the Huazhong Agricultural University, jointly trained at the Agricultural Genomics Institute at Shenzhen, Chinese Academy of Sciences, where I develop computational methods for polyploid genome assembly and chromosome-scale haplotype reconstruction.