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Table 1 Comparison of methylation analysis pipelines

From: msPIPE: a pipeline for the analysis and visualization of whole-genome bisulfite sequencing data

Pipeline Installation Quality control Alignment Methylation calling DMC/DMR analysis HMR analysis Gene function analysis Reference setting
msPIPE Docker Manual Cutadapt Trim Galore! MultiQC Bismark BS-Seeker2 Bismark BS-Seeker2 methylKit BSmooth MethylSeekR g:Profiler Automatica
BAT [33] Docker Manual BAT segemehl haarz metilene NA NA Manual
bicycle [26] Manual Docker Live CD bicycle bicycle bicycle bicycle NA NA Manual
ENCODE pipeline [34] DNAnexus Trim Galore! SAMtools Bismark Bismark Bismark NA NA NA Manual
Msuite [35] Manual Msuite Msuite Msuite NA NA NA Manual
Nextflow methylseq (Bismark) [36] Nextflow Trim Galore! MultiQC Bismark Bismark NA NA NA Automaticb
Nextflow methylseq (bwa-meth) [36] Nextflow Trim Galore! MultiQC bwa-meth MethylDackel NA NA NA Automaticb
PiGx BS-seq [37] GNU guix Trim Galore! MultiQC Bismark methylKit methylKit NA NA Manual
snakePipes [46] Bioconda Cutadapt Trim Galore! Fastp MultiQC bwa-meth MethylDackel dmrseq DSS metilene NA NA Partially automaticc
wg-blimp [47] Bioconda Docker MultiQC bwa-meth MethylDackel bsseq camel metilene MethylSeekR NA Manual
  1. NA not available
  2. aAll required files of a reference can be automatically prepared and set if the data exists in the UCSC Genome Browser database [40], and manual setting is also supported
  3. bAll required files of a reference can be automatically prepared and set if the data exists in the iGenomes database [48], and manual setting is also supported
  4. cAll required files of a reference can be automatically prepared and set if the reference is one of five species (human, mouse, zebrafish, fruit fly, and fission yeast), and manual setting is also supported