PycoQC computes metrics and generates interactive QC plots for Oxford Nanopore technologies sequencing data
Project description
pycoQC v2.5.2
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://adrienleger.com/pycoQC
Gallery
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Example HTML reports
Example JSON reports
Disclaimer
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
Classifiers
- 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
licence
GPLv3 (https://www.gnu.org/licenses/gpl-3.0.en.html)
Copyright © 2020 Adrien Leger & Tommaso Leonardi
Authors
- Adrien Leger & Tommaso Leonardi / aleg@ebi.ac.uk / https://adrienleger.com
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