ACCtools pipeline

Complete pipeline for analyzing a cancer genome using ACCtools.

Dependency

Please make anaconda environment to use SKYPE pipeline

mamba create -n skype -c conda-forge -c bioconda \
gxx cmake=3 zip psutil aria2 pyfaidx hifiasm flye minimap2 sambamba samtools \
numpy scipy matplotlib tqdm pycirclize=1.9 pandas networkx graph-tool seaborn h5py \
scikit-learn=1.6 skglm threadpoolctl

mamba activate skype
pip install juliacall

Example

git clone https://github.com/ACCtools/ACCtools-pipeline
cd ACCtools-pipeline

mamba activate skype

# Pacbio HiFi
python SKYPE.py run_hifi <Working directory> <hifi.fastq(.gz) ...>

# ONT R10 (HQ)
python SKYPE.py run_hifi --hifiasm_args="--ont" <Working directory> <hifi.fastq(.gz) ...>

# PacBio CLR
python SKYPE.py run_flye <Working directory> pacbio-raw <pacbioCLR.fastq(.gz) ...>

# ONT R9
python SKYPE.py run_flye <Working directory> nano-raw <nanoR9.fastq(.gz) ...>