PycoQC in not maintained anymore, If you are interested in continuing the delelopment of this repository please contact me to discuss an eventual ownership transfer (adrien.leger at protonmail dot com)
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 © 2020 Adrien Leger & Tommaso Leonardi
- Adrien Leger & Tommaso Leonardi