GSM-pipeline: GENE-SWitCH pipeline for comprehensive bisulfite sequencing analysis

Abstract

Abstract Background DNA methylation is a process by which methyl groups are added to the DNA molecule. Methylation of promoters influence gene expression, as the addition of a methyl group can prevent the binding of certain transcription factors and repress the transcription of the associated gene. Bioinformatics pipelines are a series of computational steps or workflows designed to analyse biological data such as sequencing data. Typically several steps, such as data preprocessing, quality control, alignment, and downstream analysis are involved. These pipelines can be tailored to a specific research question and can be customized with various software and tools. GENE-SWitCH is an EU H2020 project with the aim of providing the functional genome annotation in pig and chicken, with many different assays specifically DNA methylation. Results We present a pipeline for processing bisulfite sequencing data, which uses nf-core methylseq as a foundation. This extension pipeline includes useful steps such as analysing a bam file, methylation calling, methylation visualisation on a genome-wide level, and methylation statistics. Conclusion: Our pipeline is useful for the analysis of bisulfite sequencing data, ensuring reproducible results, and stable tool versions. It is easy to use and implement for any given data set and we executed it for analysis of > 80 RRBS and WGBS data sets.