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Table 1 Comparison of WGBS end-to-end pipelines. Most pipelines use similar software for ”standard” WGBS analysis tasks such as alignment or QC. wg-blimp improves on existing pipelines by providing a more comprehensive workflow as well as an interactive user interface

From: wg-blimp: an end-to-end analysis pipeline for whole genome bisulfite sequencing data

pipelineinstallationworkflow managementadapter trimmingalignmentmethylation callingquality controlDMR detectionsegmentationannotation
wg-blimpBioconda DockerSnakemake/bwa-methMethylDackelMultiQCbsseq camel metileneMethylSeekRCGIs genes repetitive regions
BATmanual DockerPerl/R/shell scripts/segemehlhaarzBATmetilene/arbitrary BED file
bicyclemanual Docker Live CDJava Applicationbicyclebicyclebicyclebicyclebicycle/arbitrary BED file
CpG_Me/DMRichRmanualshell/R scriptsTrim Galore!BismarkBismarkMultiQCbsseq dmrseq/CGIs genes
ENCODE pipelineDNAnexusDNAnexusTrim Galore!BismarkBismarkSAMtools Bismark//genes
Methy-PipemanualMakefileMethy-PipeMethy-PipeMethy-PipeMethy-PipeMethy-Pipe/genes
Nextflow methylseq (Bismark)NextflowNextflowTrim Galore!BismarkBismarkMultiQC///
Nextflow methylseq (bwa-meth)NextflowNextflowTrim Galore!bwa-methMethylDackelMultiQC///
PiGxGNU guixSnakemakeTrim Galore!BismarkmethylKitMultiQCmethylKitmethylKitCGIs genes
snakePipesBiocondaSnakemakeCutadapt Trim Galore! Fastpbwa-methMethylDackelMultiQCdmrseq DSS metilene/genes