相关成果发表在NAR，Zijie Jiang, Zhixiang Peng, Zhaoyuan Wei, Jiahe Sun, Yongjiang Luo, Lingzi Bie, Guoqing Zhang, Yi Wang, A deep learning-based method enables the automatic and accurate assembly of chromosome-level genomes, Nucleic Acids Research, 2024;, gkae789, https://doi.org/10.1093/nar/gkae789
githup: https://github.com/Jwindler/AutoHiC?tab=readme-ov-file
可以直接使用onehic，需要提供**hic, assembly文件，该格式通常有3d-DNA输出，对我来说3d-DNA很繁琐，较慢，因此可以直接利用bwa比对，继而获得bam文件，而后转为hic和assembly文件。
或者直接可以使用 haphic流程获得assembly以及hic。
使用onehic的流程可以参考作者所述：https://github.com/Jwindler/AutoHiC/blob/main/example/other_tools.md
#安装
# clone AutoHiC
git clone https://github.com/Jwindler/AutoHiC.git
# cd AutoHiC
cd AutoHiC
# create AutoHiC env
conda env create -f autohic.yaml
# activate AutoHiC
conda activate autohic
# configuration environment
cd ./src/models/swin
# install dependencies
pip install -e . -i https://pypi.tuna.tsinghua.edu.cn/simple/
使用onehic
# Enter the AutoHiC directory.
cd /home/ubuntu/AutoHic
# run onehic
python3.9 onehic.py -hic out.hic -asy out.assembly -autohic /home/ubuntu/AutoHic -p pretrained.pth -out ./
## 其中模型可以从作者提供的链接进行下载即可
## get new fasta
python juicebox_assembly_converter.py -a adjusted.assembly -f genome.fasta
