gemBS v4.0 (gemBS-rs) User GuideΒΆ

gemBS is a bioinformatic pipeline designed for high-throughput analysis of DNA methylation from whole genome bisulfite sequencing data (WGBS, RRBS). It combines GEM-mapper v3, a high performance read aligner and bs_call, a high performance methylation variant caller for bisulfite sequencing data into a streamlined, efficient pipeline for bisulfite sequencing analysis.

gemBS v4.0 is the latest version of the pipeline. Compared to the previous (v3.0) release, all of the applications apart from the GEM3 mapper have been re-written in Rust including the overall pipeline framework. For the pipeline framework which previously was written in Python, the move to Rust has brought speed, robustness and flexibility. For the other applications that were previously written in C, the move the Rust has brought increased reliability with not cost in speed.

You can use gemBS output for:

  • CpG and non-CpG methylation analysis

  • SNP calling from WGBS

  • Allele-specific analysis

gemBS produces summary reports (html and pdf) for quality control, .bam or .cram files with the aligned reads, .bcf files with detailed variant and methylation calling information, .bed files with methylation information at CpG and non-Cpg positions, and .bw and .bb files for visualization of methylation data in a genome browser.

The analyses performed by gemBS are compatible with the ENCODE and IHEC standard analyses (11. IHEC standard analyses) for WGBS experiments.