Detailed tutorial

We recommend users to first try the Tool showcase before this detailed tutorial. To demonstrate the toolbox applications and facilitate further understanding of the methods, we provide more detailed examples for the analysis of two datasets presented in the preprint. These datasets can be downloaded with the following commands from within a nanodisco container: get_data_bacteria and get_data_microbiome.

• 1.   Generating current differences
  • 1.1.   Preprocessing fast5 datasets
  • 1.2.   Genomic chunks information
  • 1.3.   Computing current differences
  • 1.4.   Merge current differences files
• 2.   Individual bacteria (or metagenomic bins)
  • 2.1.   De novo discovery of methylation motifs
  • 2.2.   Characterize methylation motifs: typing and fine mapping
• 3.   Microbiome (methylation binning)
  • 3.1.   Compute metagenomic contigs coverage
  • 3.2.   Compute methylation profiles
  • 3.3.   Perform methylation binning