Welcome to Nanomotif’s documentation!

Nanomotif is a Python package designed to explore methylation in prokaryotic genomes using Nanopore sequencing. Nanomotif is a fast, scalable, and sensitive tool for identification and utilization of methylation motifs in monocultures and metagenomic samples. Nanomotif offers de novo methylated motif identification, metagenomic bin contamination detection, bin association of unbinned contigs, and linking of MTase genes to methylation motifs.

Check out the Usage section for further information, including how to installation the project.

Note

This project is under active development.

• Installation
  • Conda Environment
  • Local Environment
  • Check Installation
  • MTase-linker Installation
• Required File Preparation
  • Assembly
  • Methylation Pileup
  • Contig-Bin Relationship
• Usage
  • Motif discovery
  • Bin improvement
    • Bin contamination
    • Include unbinned contigs
  • MTase-linker
• Output desciption
  • Motif Discovery
  • Bin Improvement
    • bin_contamination.tsv
    • include_contigs.tsv
  • MTase-Linker
    • mtase_assignment_table.tsv
    • nanomotif_assignment_table.tsv
  • Additional Outputs From Dependencies
• Example
  • Finding motifs in monocultures
  • Finding motifs in metagenomes with binning
  • Finding motifs in contigs
• Known issues
  • False positives around motif of other methylation types
  • High systematic 5mC noise in high GC% regions
• Troubleshooting