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

BMC Bioinformatics

Table 1 Comparison of methylation analysis pipelines

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	Automatic^a
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	Automatic^b
Nextflow methylseq (bwa-meth) [36]	Nextflow	Trim Galore! MultiQC	bwa-meth	MethylDackel	NA	NA	NA	Automatic^b
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 automatic^c
wg-blimp [47]	Bioconda Docker	MultiQC	bwa-meth	MethylDackel	bsseq camel metilene	MethylSeekR	NA	Manual

NA not available
^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
^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
^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

ISSN: 1471-2105