Commands overview

nanodisco <subtask> [options], <subtask> include:

• preprocess: Extract reads (.fasta) from base called fast5 files and map reads on reference (meta)genome
• chunk_info: Display chunks information regarding supplied reference (meta)genome
• difference: Compute nanopore signal difference between a native and a WGA dataset
• merge: Combine nanopore signal difference for all processed chunks in directory
• motif: De novo discovery of methylation motifs
• refine: Generate refine plot for candidate methylation motifs
• characterize: Predict the methylation type and fine-map the modification within the de novo discovered methylation motifs file
• coverage: Compute average coverage for each contig in a reference genome (uses bedtools genomecov)
• profile: Compute the methylation profile matrix for a metagenome sample (methylation feature at common or expected methylation motifs)
• select_feature: Select informative feature from a methylation profile matrix
• filter_profile: Compute the methylation profile matrix for selected features for a metagenome sample
• binning: Perform methylation binning, cluster metagenomic contigs according to methylation feature similarities using t-SNE
• plot_binning: Plot results of methylation binning
• score: Attribute methylation scores to each motif occurrence
• version: Plot version
• help: Print help