epiGBS2: Improvements and evaluation of highly multiplexed, epiGBS-based reduced representation bisulfite sequencing

We present epiGBS2, a laboratory protocol based on epiGBS (Gurp et al., 2016) with a revised and user-friendly bioinformatics pipeline for a wide range of species with or without reference genome. Performance of several critical steps in epiGBS2 was evaluated against baseline data sets from <em>Arabidopsis thaliana</em> and Great tit (<em>Parus major</em>), which confirmed overall good performance of epiGBS2. We provide here the raw bisulfite sequencing data of the epiGBS2 run for <em>Arabidopsis thaliana.</em> A detailed description of the laboratory protocol and an extensive manual of the bioinformatics pipeline are publicly accessible on github (https://github.com/nioo-knaw/epiGBS2) and zenodo (https://doi.org/10.5281/zenodo.4764652). Demultiplexed data were deposited on NCBI under the BioProject ID PRJNA764918