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pycoqc website  

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+.

Environment Modules

Run module spider pycoqc to find out what environment modules are available for this application.

System Variables

  • HPC_PYCOQC_DIR - installation directory


If you publish research that uses pycoqc you have to cite it as follows:

Leger et al., (2019). pycoQC, interactive quality control for Oxford Nanopore Sequencing. Journal of Open Source Software, 4(34), 1236,