Oxford Nanopore sequencing enables detection of several naturally occurring and synthetic DNA and RNA modifications, including 5mC, 5hmC, 4mC, 6mA, m6A, pseudoU, inosine, m5C and 2'-O-Me(U/C/A/G). Please refer to the Accuracy page for the full list of supported modifications.

It is possible to detect the modified bases directly from the signal data when the appropriate PCR-free protocols have been used, providing additional insight into biological data even when not directly the goal of an experiment. Detecting a modified base typically requires a dedicated model for the specific modified base.

Both MinKNOW and Dorado include models and options for detecting modified bases from the signal data generated during Oxford nanopore sequencing. When detecting methylation with these tools, please ensure that you output a BAM-formatted file, as methylation information is stored in the BAM format.

The modified information stored in the BAM files can be further processed using the modkit tool, which is also included in the wf-human-variation analysis workflow.

If you are using third-party tools, please consult their respective GitHub pages for installation instructions and usage guidelines. We are unable to provide support for third-party software. For assistance, post any questions or issues to the Issues tab on the relevant GitHub repository.