pycoQC 2.5.2

PycoQC computes metrics and generates interactive QC plots for Oxford Nanopore technologies sequencing data

pycoQC v2.5.2

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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

• Albacore_all_RNA

• Guppy-2.1.3_basecall-1D_RNA

• Guppy-2.3_basecall-1D_alignment-DNA

• Albacore-1.2.1_basecall-1D-DNA

• Guppy-2.1.3_basecall-1D_DNA_barcode

• Albacore-1.7.0_basecall-1D-DNA_API

• Albacore-2.1.10_basecall-1D-DNA

• Albacore-1.7.0_basecall-1D-DNA

Example JSON reports

• Guppy-2.3_basecall-1D_alignment-DNA

• Guppy-2.1.3_basecall-1D_RNA

• Albacore-1.7.0_basecall-1D-DNA_API

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 / [e-mail] / https://adrienleger.com