MethGo: a comprehensive tool for analyzing whole-genome bisulfite sequencing data

Area of Science:

• Epigenetics
• Genomics
• Bioinformatics

Background:

• DNA methylation is a key epigenetic regulator of biological processes.
• Bisulfite sequencing (BS-Seq) is a standard method for measuring DNA methylation genome-wide at single-base resolution.
• BS-Seq data analysis requires specialized aligners and bioinformatics pipelines.

Purpose of the Study:

• To develop MethGo, a user-friendly software tool for analyzing whole-genome bisulfite sequencing (WGBS) and reduced representation bisulfite sequencing (RRBS) data.
• To provide a comprehensive suite of genomic and epigenomic analyses for BS-Seq data.

Main Methods:

• Development of MethGo, a Python-based software tool.
• Implementation of 9 distinct analytical modules within MethGo.
• Integration of capabilities for analyzing DNA methylation, transcription factor binding sites, single nucleotide polymorphisms (SNPs), and copy number variations (CNVs).

Main Results:

• MethGo offers 9 analyses across 5 major modules for comprehensive (epi)genome profiling.
• The tool enables analysis of global and gene-level DNA methylation patterns.
• MethGo facilitates the assessment of methylation patterns at transcription factor binding sites (TFBSs) and detects genetic variations like SNPs and CNVs.

Conclusions:

• MethGo is an effective and straightforward tool for BS-Seq data analysis (WGBS and RRBS).
• It provides extensive profiling of DNA methylation at both global and gene scales.
• The software supports the analysis of methylation patterns around TFBSs and identifies genetic variations.