ONT MDI Tools

The Michigan Data Interface (MDI) is a standardized framework for developing, installing and running HPC data analysis pipelines and interactive R Shiny visualization applications.

This ont-mdi-tools repository contains pipelines and apps from the Thomas Wilson laboratory at the University of Michigan for general processing of Oxford Nanopore read data, including activities like basecalling, POD5 file manipulation, modification modeling, etc.

In general, these tools implement publicly distributed ONT software and act upstream of genome-specific actions like alignment and variant calling.

Available tools

Pipelines and apps in stable release, based on established modules:

• ont = a simple pipeline wrapper around download, convert, condense, repack, and basecall actions

Pipelines and apps in alpha, with exploratory code that is not considered stable:

• modmod = train a base modification model (modmod) using concatemerized oligos

Shared action modules for use by other pipelines include:

• download = downlad ONT software and basecalling models
• convert = convert FAST5 files to POD5 format
• condense = reduce the number of POD5 files in an ONT flowcell run
• filter = filter POD5 files against a set of read ids
• repack = sort a set of POD5 files from a single ONT run to one POD5 file per channel group prior to duplex analysis
• basecall = perform efficient basecalling (and optionally alignment) on POD5 reads on a shared compute cluster

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For more information about the MDI, please visit:

MDI Documentation MDI Basic Training MDI GitHub page

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