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Table 1 The comparisons of EpiMOLAS with other platforms and tools on the WGBS analysis

From: EpiMOLAS: an intuitive web-based framework for genome-wide DNA methylation analysis

 

EpiMOLAS

BAT

ENCODE-WGBS

snakePipe

NGI-MethylSeq

Mint

MethylPipe

MethylSig

Methylkit

Environment

Docker|Galaxy web server

Docker

Shell script

Bioconda Snakemake

Docker Nextflow

Galaxy

R package

R package

R package

Sequence context

CGCHG, CHH

CG

CG, CHG, CHH

CG, CHG, CHH

CG, CHG, CHH

CG

CG, CHG, CHH

CG, CHG, CHH

CG, CHG, CHH

Start with

raw reads

raw reads

raw reads

raw reads

raw reads

raw reads

methylation call file

methylation call file

methylation call file

Docker container

DocMethyl

+

+

–

–

+

–

NA

NA

NA

Web interface

+ (Galaxy)

–

+

–

–

+ (Galaxy)

NA

NA

NA

Adapter and base quality trimming a

+

–

+

+

+

+

NA

NA

NA

QC report b

+

+

+

+

+

+

NA

NA

NA

Read mapping c

+

+

+

+

+

+

NA

NA

NA

Methylation sites calling c

+

+

+

+

+

+

NA

NA

NA

Discriptive statistics

EpiMOLAS_web

+

+

–

+

+

+

+

+

+

Find DMRs d

+ (simple)

+ (metilene)

–

+ (metilene)

–

+ (DSS)

+

+

+

Clustering Analysis

+ (heatmap)

+ (heatmap)

–

+ (heatmap)

–

–

–

+ (heatmap)

–

GO term enrichment

+

–

–

–

–

–

+

–

–

KEGG pathway enrichment

+

–

–

–

–

–

–

–

–

TFBS enrichment

–

–

–

–

–

–

–

+

–

Genome-wide visualization

+ (circos plot)

+ (circos plot)

–

–

–

–

–

–

–

Interacitve Quantitative Analysis

+

–

–

–

–

–

NA

NA

NA

Data browsing and retrieving UI

+

–

–

–

–

–

NA

NA

NA

Gene list with tracking logs

+

–

–

–

–

–

NA

NA

NA

Venn analysis on gene lists

+

–

–

–

–

–

–

–

–

Interplay with other high throughput data

Protein Interactome e

transcriptome

–

RNA-seq, ChIP-seq, ATAC-seq, Hi-C etc.

–

hydroxyl-methylation data

RNA-seq, ChIP-seq, DNase-seq

–

–

  1. Remarks: aEpiMOLAS, ENCODE-WGBS, snakePipe, NGI-MethylSeq and Mint adopt Trim Galore/cutadapt in the workflow for adapter and base quality trimming
  2. bEpiMOLAS, snakePipe, NGI-MethylSeq and Mint integrate FASTQC to report read quality. BAT includes BSeQC for BS-seq experiment quality assessment.ENCODE-WGBS collects samtools and Bismark metrics as quality reports
  3. cEpiMOLAS, ENCODE-WGBS and Mint mainly use Bismark in the workflow for alignment and methylation extraction. BAT uses segemehl and in-houseBAT_calling tools. snakePipe adopts bwa-meth for alignment and MethylDackel for methylation calling. NGI-MethylSeq provides two data analysisworkflows for choices: Bismark and bwa-meth/MethylDackel
  4. dEpiMOLAS uses simple method for DMGs. BAT and snakePipe include metilene for DMRs. Mint integrates DSS for DMRs
  5. eEpiMOLAS includes a dedicated plugin viewer to explore the protein interaction network