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Work in progress

mako is in active development. While the core pipeline has been implemented and tested, not all features are supported yet (e.g. metagene plot, etc.) Bug reports are highly welcome and we would greatly appreciate they be sent to our GitHub Issues tracker.

Mako is a bioinformatics pipeline designed for isoform-level analysis of differential RNA modifications 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 (adaptive, default; refer to code for decision logic)
   2. Binomial (binomial)
   3. Beta-binomial (beta_binomial)
   4. DSS (dss)
4. False discovery rate correction
5. Visualization of results via makoview

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