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Mako is a bioinformatics pipeline designed for differential RNA modification analysis at the isoform resolution using Nanopore direct RNA sequencing. It takes a samplesheet and output from Dorado and/or m6Anet, and applies various statistical methods to identify differentially modified sites between experimental conditions.

Mako will also produce interactive visualisations for quality control and assessment of sites through the makoview tool.

The software is written in Nextflow and utilises Docker/Singularity containerisation for reproducibility and ease of installation.

Tip

See Getting Started for a tutorial with provided example data.

See Installation and Usage respectively for installing and running the pipeline.

Steps of the pipeline

1. Sample and read QC
2. Site-level aggregation, filtering, and selection
3. Choice of differential analysis methods:
   1. Either binomial or beta-binomial, depending on the dispersion (default)
   2. Binomial
   3. Beta-binomial
4. False discovery rate correction
5. Visualization of results via makoview

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