ArticleMolecular ecology resources2022
epiGBS2: Improvements and evaluation of highly multiplexed, epiGBS-based reduced representation bisulfite sequencing.
Article in Molecular ecology resources, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. An erratum has been issued. Cited by 11 papers.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
11 citing papers in PubMed.
- Independent Avian Epigenetic Clocks for Ageing and Development.Molecular ecology resources · 2025Article
- Introduction of epigenetic variation contribute to resistance against the human parasite Schistosoma mansoni.Epigenetics & chromatin · 2025Article
- DNA Methylation Associates With Sex-Specific Effects of Experimentally Increased Yolk Testosterone in Wild Nestlings.Molecular ecology · 2025Article
- Assessing Rapid Adaptation Through Epigenetic Inheritance: A New Experimental Approach.Plant, cell & environment · 2025Article
- Epigenetic differences between wild and cultivated grapevines highlight the contribution of DNA methylation during crop domestication.BMC plant biology · 2024Article
- Early developmental carry-over effects on exploratory behaviour and DNA methylation in wild great tits (Evolutionary applications · 2024Article
- Variation in DNA Methylation in Avian Nestlings Is Largely Determined by Genetic Effects.Molecular biology and evolution · 2023Article
- Herbivory induced methylation changes in the Lombardy poplar: A comparison of results obtained by epiGBS and WGBS.PloS one · 2023Article
- DNA methylation in clonal duckweed (Lemna minor L.) lineages reflects current and historical environmental exposures.Molecular ecology · 2023Article
- epiGBS2: Improvements and evaluation of highly multiplexed, epiGBS-based reduced representation bisulfite sequencing.Molecular ecology resources · 2022Article
- Manipulating base quality scores enables variant calling from bisulfite sequencing alignments using conventional bayesian approaches.BMC genomics · 2022Article
Corrections and comments
- Erratum issued
Authors and funding
14 authors.
Funding
Abstract
Several reduced-representation bisulfite sequencing methods have been developed in recent years to determine cytosine methylation de novo 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 Snakemake workflow management system, which makes the pipeline easy to execute and modular, and parameter settings for important computational steps flexible. We implemented bismark for alignment and methylation analysis and we preprocessed alignment files by double masking to enable single nucleotide polymorphism calling with Freebayes (epiFreebayes). The performance of several critical steps in epiGBS2 was evaluated against baseline data sets from Arabidopsis thaliana and great tit (Parus major), 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 (https://github.com/nioo-knaw/epiGBS2) and zenodo (https://doi.org/10.5281/zenodo.4764652).
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.