Figure 1

Experimental workflow for population epigenomic profiling using sounDMR. Multiplexing along with adaptive sampling on Oxford Nanopore devices allows for the relatively rapid and inexpensive sequencing of large numbers of individuals (shown here 8 individuals, that would be barcoded separately and multiplexed for sequencing, however this number would vary depending on the user's experimental design). Using tools already available we perform basecalling and methylation calling from this sequencing data. After individual methylomes have been established, our new package sounDMR combines these into a single project file and allows for statistical analyses using a flexible mixed modeling framework to compare methylation between groups of individuals, or specific clones of interest. Additionally, this pipeline makes it easy to estimate within group epigenetic variance at a per-cytosine level, enabling hyper-variable epigenomic regions to be identified. This data is all output into a unified output data frame that enables downstream analysis into population epigenomic patterns.