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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

 EpiMOLASBATENCODE-WGBSsnakePipeNGI-MethylSeqMintMethylPipeMethylSigMethylkit
EnvironmentDocker|Galaxy web serverDockerShell scriptBioconda SnakemakeDocker NextflowGalaxyR packageR packageR package
Sequence contextCGCHG, CHHCGCG, CHG, CHHCG, CHG, CHHCG, CHG, CHHCGCG, CHG, CHHCG, CHG, CHHCG, CHG, CHH
Start withraw readsraw readsraw readsraw readsraw readsraw readsmethylation call filemethylation call filemethylation call file
Docker containerDocMethyl+++NANANA
Web interface+ (Galaxy)++ (Galaxy)NANANA
Adapter and base quality trimming a+++++NANANA
QC report b++++++NANANA
Read mapping c++++++NANANA
Methylation sites calling c++++++NANANA
Discriptive statisticsEpiMOLAS_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+NANANA
Data browsing and retrieving UI+NANANA
Gene list with tracking logs+NANANA
Venn analysis on gene lists+
Interplay with other high throughput dataProtein Interactome etranscriptomeRNA-seq, ChIP-seq, ATAC-seq, Hi-C etc.hydroxyl-methylation dataRNA-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