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C-Phasing

Phasing and scaffolding polyploid genomes based on Pore-C, 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, 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 data. It also works on Hi-C data and diploid genome assembly.

The advantages of C-Phasing:
- High speed.
- High anchor rate of genome.
- High accuracy of polyploid phasing.

Installation#

Download the CPhasing and activate environments by the activate_cphasing 

git clone https://github.com/wangyibin/CPhasing.git 

./CPhasing/bin/activate_cphasing

Note

For the first configuration, run it when the network is accessible.

Note

If you do not have direct access to the anaconda repository, you can set the mirror for pixi.

Download the CPhasing and install environment by conda 

git clone https://github.com/wangyibin/CPhasing.git

cd CPhasing
conda env create -f environment.yml
conda activate cphasing
Add the following to the ~/.bash_profile
~/.bash_profile
export PATH=/path/to/CPhasing/bin:$PATH
export PYTHONPATH=/path/to/CPhasing:$PYTHONPATH

Note

The hic pipeline require GLIBCXX_3.4.29, or you can add the following to the start of cphasing execute script, e.g.: run.sh

run.sh
export LD_LIBRARY_PATH=/path/to/anaconda3/envs/cphasing/lib:$LD_LIBRARY_PATH

Install C-Phasing#

## Download C-Phasing and install python dependencies
git clone https://github.com/wangyibin/CPhasing.git
cd CPhasing
pip install .
Add following to the ~/.bash_profile or ~/.bashrc
~/.bash_profile
export PATH=/path/to/CPhasing/bin:$PATH

Dependencies#

  1. For core function
    - bedtools
    - seqkit
    - pigz
  2. For Pore-C pipeline
    - minimap2(>= v2.24)
  • Basic Usage

    Use pipeline to run cphasing.

    Basic Usage

  • Tutorials

    Tutorials to help you know how to run cphasing.
    Tutorials