EpiDiverse/ewas is a bioinformatics analysis pipeline for performing epigenome-wide association studies from methylated positions and/or regions, with optional analysis of methQTLs for diploid organisms from variant call data.

The workflow processes a population of sample bed files, usually derived from the EpiDiverse-WGBS pipeline, and formats them with bedtools for analysis with the R package GEM. Output in the form of DMPs or DMRs from the EpiDiverse-DMR pipeline can also be given to pre-filter the number of positions and reduce multiple comparisons. In addition, the union set of DMRs can themselves be used as independent markers within EWAS in place of individual positions. Sample variants, usually derived from the EpiDiverse-SNP pipeline, can additionally be provided to test the association of methylation-SNP pairs as methQTLs. The pipeline provides visualisation in the form of Manhattan plots for Emodel, sequence dotplots for Gmodel, genotype interaction plots for GxE model, and p-value QQ-plots + histograms for all models, each with ggplot2.

See the output documentation for more details of the results.

The pipeline is built using Nextflow, a workflow tool to run tasks across multiple compute infrastructures in a very portable manner. It comes with docker containers making installation trivial and results highly reproducible.

1. Install nextflow

2. Install one of docker, singularity or conda

3. Download the pipeline and test it on a minimal dataset with a single command

NXF_VER=20.07.1 nextflow run epidiverse/ewas -profile test,<docker|singularity|conda>

4. Start running your own analysis!

NXF_VER=20.07.1 nextflow run epidiverse/ewas -profile <docker|singularity|conda> \
--input /path/to/wgbs/directory --samples /path/to/samples.tsv

See the usage documentation for all of the available options when running the pipeline.

The EpiDiverse/template pipeline is part of the EpiDiverse Toolkit, a best practice suite of tools intended for the study of Ecological Plant Epigenetics. Links to general guidelines and pipeline-specific documentation can be found below:

1. Installation
2. Pipeline configuration
   • Local installation
   • Adding your own system config
   • EpiDiverse infrastructure
3. Running the pipeline
4. Understanding the results
5. Troubleshooting

These scripts were originally written for use by the EpiDiverse European Training Network, by Adam Nunn (@bio15anu) and Nilay Can (@nilaycan).

This project has received funding from the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie grant agreement No 764965

If you use epidiverse/ewas for your analysis, please cite it using the following doi: