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

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Bisulfite Representation (politics) Computational biology Multiplexing Computer science Bisulfite sequencing Chemistry Biology DNA methylation Biochemistry Telecommunications Gene Politics Law Political science Gene expression

Fleur Gawehns , Maarten Postuma , Morgane Van Antro , Adam Nunn , Bernice Sepers , Samar Fatma , Thomas P. van Gurp , Niels Wagemaker , A. Christa Mateman , Slavica Milanovic‐Ivanovic , Ivo Große , Kees van Oers , Philippine Vergeer , Koen J. F. Verhoeven ·

YOU? · · 2021 · Open Access · · DOI: https://doi.org/10.5281/zenodo.5519370 · OA: W4393720982

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 Arabidopsis thaliana and Great tit (Parus major), which confirmed overall good performance of epiGBS2. We provide here the raw bisulfite sequencing data of the epiGBS2 run for Arabidopsis thaliana. 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).