HiFi-SR is a Python-based pipeline for the detection of plant mitochondrial structural rearrangements based on the mapping of PacBio high-fidelity (HiFi) reads or Circular Consensus Sequencing (ccs) data, to a reference genome (i.e., the hypothetical master cycle DNA).
We are currently making significant upgrades and modifications to hifisr to enhance its functionality and performance. During this period, please use the old version v.0.2.0, temporarily.
Deps
The pipeline has been tested in WSL2 distribution Ubuntu-20.04. It shall work in other Linux operating system, such as CentOS.
- Download the hifisr repository
git clone https://github.com/zouyinstein/hifisr
- Create and activate a conda environment.
conda create -n hifisr python=3.13
conda activate hifisr
- Use Anaconda3 to install required packages.
conda install pigz -c conda-forge
conda install samtools bamtools blast seqkit parafly -c bioconda
# create a soft link to ensure samtools can work
ln -sf ${HOME}/.conda/envs/hifisr/lib/libcrypto.so.1.1 ${HOME}/.conda/envs/hifisr/lib/libcrypto.so.1.0.0
- Install bcftools demo
- Install minimap2
cd hifisr/deps
curl -L https://github.com/lh3/minimap2/releases/download/v2.24/minimap2-2.24_x64-linux.tar.bz2 | tar -jxvf -
./minimap2-2.24_x64-linux/minimap2
- Install MECAT2
cd hifisr/deps
git clone https://github.com/xiaochuanle/MECAT2.git
cd MECAT2
make -j
export PATH="$PWD/deps/MECAT2/Linux-amd64/bin:$PATH"
- Install metaFlye
cd hifisr/deps
git clone https://github.com/fenderglass/Flye
cd Flye
python setup.py install
- Install required Python packages
pip install biopython pandas openpyxl
Test
# Make sure the HiFi-SR repository has been downloaded (git clone https://github.com/zouyinstein/hifisr).
# Make sure the hifisr environment has been activated (conda activate hifisr).
# Make sure the dependent third-party softwares/packages has been installed.
# Change working directory to hifisr
Description of results
demo
Example 1
Analyze of an example wild-type Arabidopsis thaliana dataset Col-CEN (ERR6210723, 14.6 Gb, Naish et al., 2021, Science):