epiGBS2

epiGBS2 enables de novo determination of cytosine methylation patterns and genetic polymorphisms from reduced representation bisulfite sequencing (RRBS) data across diverse species.

Key Features:

• Reduced representation bisulfite sequencing (RRBS): Implements an RRBS-based approach to interrogate DNA methylation at cytosines.
• De novo methylation and variant detection: Simultaneously determines cytosine methylation patterns and genetic polymorphisms without requiring a reference genome.
• Flexible restriction enzyme selection: Library preparation supports choice of restriction enzymes, including an option for double digest strategies to tailor representation of the genome.
• Semi-methylated adapters: Uses semi-methylated adapters in library preparation as an alternative to fully methylated adapters.
• Automated bioinformatics pipeline: Provides an automated processing pipeline for bisulfite sequencing data integrated into the Snakemake workflow system.
• Parameter customization: Pipeline parameters can be adjusted to accommodate different experimental designs and species genomes.

Scientific Applications:

• Epigenetic studies: Generates methylation profiles for studies of DNA methylation dynamics and regulation.
• Evolutionary biology: Enables assessment of methylation and genetic variation for comparative and evolutionary analyses.
• Comparative genomics: Facilitates cross-species comparison of methylation patterns and polymorphisms, including species lacking reference genomes.
• Gene–environment and developmental studies: Supports investigation of gene–environment interactions and developmental processes involving DNA methylation.
• Disease mechanism research: Provides methylation and genetic variant data relevant to studies of disease-associated epigenetic changes.

Methodology:

An automated bioinformatics pipeline integrated into Snakemake processes raw bisulfite sequencing reads to produce cytosine methylation and genetic polymorphism outputs.