C-Phasing
Phasing and scaffolding polyploid genomes based on Pore-C, HiFi-C(CiFi), Ultra-long, or Hi-C data
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Introduction¶
One of the major problems with Hi-C scaffolding of polyploid genomes is a large proportion of ambiguous short-read mapping, leading to a high-level of switched or chimeric assemblies. Now, the long-read-based chromosome conformation capture technology, e.g., Pore-C, HiFi-C, provides an effective way to overcome this problem. Here, we developed a new pipeline, namely C-Phasing, which is specifically tailored for polyploid phasing by leveraging the advantage of Pore-C or HiFi-C data. It also works on Hi-C (or other 3C technologies, e.g. Omni-C and Micro-C) data and diploid genome assembly.
The advantages of C-Phasing:
- High speed.
- High anchor rate of genome.
- High accuracy of polyploid phasing.
- Basic Usage