pycoQC 2.5.1

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

Full documentation is available at https://a-slide.github.io/pycoQC/

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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 generates a summary file from basecalled fast5 files. The package supports 1D and 1D2 runs generated with Minion, Gridion and Promethion devices and basecalled with Albacore 1.2.1+ or Guppy 2.1.3+. PycoQC is written in pure Python3. Python 2 is not supported.

Great tutorial with detailed explanations by Tim Kahlke available at https://timkahlke.github.io/LongRead_tutorials/QC_P.html

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

Authors

• Adrien Leger - aleg {at} ebi.ac.uk

• Tommaso Leonardi - tom {at} tleo.io