https://wangyibin.github.io/tags/rust/RustHugoBlox Kit (https://hugoblox.com)en-ushttps://wangyibin.github.io/media/icon.svghttps://wangyibin.github.io/tags/rust/https://wangyibin.github.io/projects/c-phasing/Mon, 01 Jan 0001 00:00:00 +0000https://wangyibin.github.io/projects/c-phasing/<h2 id="overview">Overview</h2> <p>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.</p> <p>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.</p> <h2 id="key-features">Key Features</h2> <ul> <li>Hypergraph-based chromosome partitioning using multi-way chromatin interactions</li> <li>Support for both Hi-C and Pore-C data</li> <li>Methylation-assisted alignment refinement (MethAlign)</li> <li>Chimeric contig detection (Hitig)</li> <li>Copy-number-aware collapsed contig rescue (CollapseRescue)</li> <li>Chromosome-scale scaffolding for complex polyploid genomes</li> </ul> <h2 id="applications">Applications</h2> <p>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.</p> <h2 id="resources">Resources</h2> <ul> <li>Source code: </li> <li>Documentation: <em> </em></li> <li>Manuscript: <em>(under submit)</em></li> </ul>