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 | – | – |