Version Compatibility

Reference examples tested with: methylKit 1.28+, minimap2 2.26+, samtools 1.19+

Before using code patterns, verify installed versions match. If versions differ:

• CLI: <tool> --version then <tool> --help to confirm flags

If code throws ImportError, AttributeError, or TypeError, introspect the installed package and adapt the example to match the actual API rather than retrying.

Nanopore Methylation Calling

"Call methylation from my Nanopore reads" → Extract 5mC/6mA modification probabilities from basecalled reads and summarize per-site methylation frequencies.

• CLI: modkit pileup aligned.bam methylation.bed --ref ref.fa

Modern Workflow (modkit)

ONT's modkit is the recommended tool for methylation analysis from basecalled data.