PycoQC computes metrics and generates interactive QC plots for Oxford Nanopore technologies sequencing data
PycoQC relies on the sequencing_summary.txt file generated by Albacore and Guppy, but if needed it can also generate a summary file from basecalled fast5 files. The package supports 1D and 1D2 runs generated with Minion, Gridion and Promethion devices, basecalled with Albacore 1.2.1+ or Guppy 2.1.3+. PycoQC is written in pure Python3. Python 2 is not supported. For a quick introduction see tutorial by Tim Kahlke available at https://timkahlke.github.io/LongRead_tutorials/QC_P.html
Full documentation is available at https://a-slide.github.io/pycoQC
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Please be aware that pycoQC is a research package that is still under development.
It was tested under Linux Ubuntu 16.04 and in an HPC environment running under Red Hat Enterprise 7.1.
Thank you
- Development Status :: 3 - Alpha
- Intended Audience :: Science/Research
- Topic :: Scientific/Engineering :: Bio-Informatics
- License :: OSI Approved :: GNU General Public License v3 (GPLv3)
- Programming Language :: Python :: 3
GPLv3 (https://www.gnu.org/licenses/gpl-3.0.en.html)
Copyright © 2023 Adrien Leger, Tommaso Leonardi & Marc-Olivier Duceppe
- Adrien Leger, Tommaso Leonardi & Marc-Olivier Duceppe / aleg@ebi.ac.uk / https://adrienleger.com
# Install miniconda
wget https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh
chmod +x Miniconda3-latest-Linux-x86_64.sh
./Miniconda3-latest-Linux-x86_64.sh # Accept ELUA, install in default location and say "yes" to have it start autumatically
rm Miniconda3-latest-Linux-x86_64.sh
# Apply changes
source ~/.bashrc
# Add channels
# Order is important here
conda config --add channels defaults
conda config --add channels plotly
conda config --add channels bioconda
conda config --add channels conda-forge
# Install mamba
conda install mamba
mamba create -n pycoQC -y python=3 cython
conda activate pycoQC
[ -d $HOME/prog ] || mkdir -p $HOME/prog
cd $HOME/prog
git clone https://github.com/duceppemo/pycoQC
cd pycoQC
python setup.py install
pip install pod5
# Test installation
# Should display help message with no errors
pycoQC -h
# If you get an error, try to to run the following command
# https://numpy.org/devdocs/user/troubleshooting-importerror.html#downstream-importerror-or-attributeerror
pip install pyarrow --upgrade