epiGBS2: Improvements and evaluation of highly multiplexed, epiGBS-based reduced representation bisulfite sequencing.
DNA methylation
SNP calling
bisulfite sequencing
de novo reference
double digest
nonmodel species
reduced representation
Journal
Molecular ecology resources
ISSN: 1755-0998
Titre abrégé: Mol Ecol Resour
Pays: England
ID NLM: 101465604
Informations de publication
Date de publication:
Jul 2022
Jul 2022
Historique:
revised:
04
02
2022
received:
12
11
2021
accepted:
09
02
2022
pubmed:
19
2
2022
medline:
9
6
2022
entrez:
18
2
2022
Statut:
ppublish
Résumé
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).
Identifiants
pubmed: 35178872
doi: 10.1111/1755-0998.13597
pmc: PMC9311447
doi:
Substances chimiques
Sulfites
0
hydrogen sulfite
OJ9787WBLU
Types de publication
Journal Article
Langues
eng
Sous-ensembles de citation
IM
Pagination
2087-2104Subventions
Organisme : EU Horizon 2020 programme under Marie Skłodowska-Curie
ID : 764965
Organisme : Aspasia
Organisme : NWO Open Competition
ID : ALWOP.314
Informations de copyright
© 2022 The Authors. Molecular Ecology Resources published by John Wiley & Sons Ltd.
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