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Alternative and complementary packages

Here is a non-exhaustive list of alternative/complementary packages that could also be used to QC Nanopore sequencing data:

  • Nanoplot: Generic QC. Part of NanoPack metapackage which offers a broad range of functionalities. (Python)
  • MinION-QC: Generic QC with additional interesting plots such as flowcell_overview. (R)
  • toullig-QC: Generic QC. Requires additional input files but gives base resolution information (Python)
  • flowcellvis: Animated GIF of flow cell performance. (Python)
  • Basic QC Tutorial: Provided by ONT. Step by step hands-on guide to perform a basic quality control of sequencing data. (R)

pycoQC results are consistent with other packages. Reports of the same datasets generated by Nanoplot, MinIONQC and pycoQC are available at the following URL: https://www.ebi.ac.uk/~aleg/data/pycoQC_test/comparison/