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

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

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  • Medientyp: E-Artikel
  • Titel: epiGBS2: Improvements and evaluation of highly multiplexed, epiGBS‐based reduced representation bisulfite sequencing
  • Beteiligte: Gawehns, Fleur; Postuma, Maarten; van Antro, Morgane; Nunn, Adam; Sepers, Bernice; Fatma, Samar; van Gurp, Thomas P.; Wagemaker, Niels C. A. M.; Mateman, A. Christa; Milanovic‐Ivanovic, Slavica; Groβe, Ivo; van Oers, Kees; Vergeer, Philippine; Verhoeven, Koen J. F.
  • Erschienen: Wiley, 2022
  • Erschienen in: Molecular Ecology Resources
  • Sprache: Englisch
  • DOI: 10.1111/1755-0998.13597
  • ISSN: 1755-098X; 1755-0998
  • Entstehung:
  • Anmerkungen:
  • Beschreibung: <jats:title>Abstract</jats:title><jats:p>Several reduced‐representation bisulfite sequencing methods have been developed in recent years to determine cytosine methylation <jats:italic>de novo</jats:italic> in nonmodel species. Here, we present epiGBS2, a laboratory protocol based on epiGBS with a revised and user‐friendly bioinformatics pipeline for a wide range of species with or without a reference genome. epiGBS2 is cost‐ and time‐efficient and the computational workflow is designed in a user‐friendly and reproducible manner. The library protocol allows a flexible choice of restriction enzymes and a double digest. The bioinformatics pipeline was integrated in the <jats:sc>Snakemake</jats:sc> workflow management system, which makes the pipeline easy to execute and modular, and parameter settings for important computational steps flexible. We implemented <jats:sc>bismark</jats:sc> for alignment and methylation analysis and we preprocessed alignment files by double masking to enable single nucleotide polymorphism calling with <jats:sc>Freebayes</jats:sc> (<jats:sc>epiFreebayes</jats:sc>). The performance of several critical steps in epiGBS2 was evaluated against baseline data sets from <jats:italic>Arabidopsis thaliana</jats:italic> and great tit (<jats:italic>Parus major</jats:italic>), which confirmed its overall good performance. We provide a detailed description of the laboratory protocol and an extensive manual of the bioinformatics pipeline, which is publicly accessible on github (<jats:ext-link xmlns:xlink="http://www.w3.org/1999/xlink" xlink:href="https://github.com/nioo-knaw/epiGBS2">https://github.com/nioo‐knaw/epiGBS2</jats:ext-link>) and zenodo (<jats:ext-link xmlns:xlink="http://www.w3.org/1999/xlink" xlink:href="https://doi.org/10.5281/zenodo.4764652">https://doi.org/10.5281/zenodo.4764652</jats:ext-link>).</jats:p>