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
pipeline | installation | workflow management | adapter trimming | alignment | methylation calling | quality control | DMR detection | segmentation | annotation |
|---|---|---|---|---|---|---|---|---|---|
wg-blimp | Bioconda Docker | Snakemake | / | bwa-meth | MethylDackel | MultiQC | bsseq camel metilene | MethylSeekR | CGIs genes repetitive regions |
BAT | manual Docker | Perl/R/shell scripts | / | segemehl | haarz | BAT | metilene | / | arbitrary BED file |
bicycle | manual Docker Live CD | Java Application | bicycle | bicycle | bicycle | bicycle | bicycle | / | arbitrary BED file |
CpG_Me/DMRichR | manual | shell/R scripts | Trim Galore! | Bismark | Bismark | MultiQC | bsseq dmrseq | / | CGIs genes |
ENCODE pipeline | DNAnexus | DNAnexus | Trim Galore! | Bismark | Bismark | SAMtools Bismark | / | / | genes |
Methy-Pipe | manual | Makefile | Methy-Pipe | Methy-Pipe | Methy-Pipe | Methy-Pipe | Methy-Pipe | / | genes |
Nextflow methylseq (Bismark) | Nextflow | Nextflow | Trim Galore! | Bismark | Bismark | MultiQC | / | / | / |
Nextflow methylseq (bwa-meth) | Nextflow | Nextflow | Trim Galore! | bwa-meth | MethylDackel | MultiQC | / | / | / |
PiGx | GNU guix | Snakemake | Trim Galore! | Bismark | methylKit | MultiQC | methylKit | methylKit | CGIs genes |
snakePipes | Bioconda | Snakemake | Cutadapt Trim Galore! Fastp | bwa-meth | MethylDackel | MultiQC | dmrseq DSS metilene | / | genes |