Link Search Menu Expand Document

Wrapper pipeline: ont

The ont pipeline has no larger purpose, it is a simple wrapper around some of the core actions provided by the ont-mdi-tools repository, namely:

  • download ONT software and models
  • convert FAST5 to POD5 files
  • condense the number of POD5 files in an ONT flowcell run
  • repack time-series POD5 files from MinKnow by channel group for duplex analysis
  • basecall POD5 signal data in simplex or duplex mode

Most actions are wrappers that help you run ONT software such as pod5 and dorado correctly and efficiently. They are not separate implementations of these program functions.

Developers of more complex MDI pipelines with bigger downstream goals can use ont as a template to get started, since many of these same steps will start most ONT pipelines.

Usage

See our general installation and usage help and:

mdi --help
mdi ont --help
mdi ont basecall --help # etc.