Selected tool | Experimental approach | From raw reads to DMPs and DMRs | Graphic output | Detailed manual available | Reference | |||
---|---|---|---|---|---|---|---|---|
Quality control and 3′ trimming | Alignment | Methylation levels | Differential methylation | |||||
BSmooth | WGBS | No | Yes | Yes | DMRs only | BED, bedGraph, Tab-del | Yes | [51] |
MOABS | WGBS, RRBS, and possibly 5hmC seq | Yes | Yes | Yes, but no beta score | Yes | BED, bedGraph, Tab-del | Yes | [52] |
MethPipe | WGBS and 5hmC seq | Error estimation only | Yes | Yes | Yes | BED, bedGraph, Tab-del | Yes | [53] |
Bicycle* | WGBS and 5hmC seq | Yes | Yes | Yes | Yes | BED, bedGraph, Tab-del, VCF | Yes | [54] |
SMAP* | RRBS only | Trimming only | Yes | Yes | Yes, also SNPs | Tab-del | Yes | [55] |
Genestack.com (web-based) | WGBS and RRBS | Yes | Yes | Yes | No | Yes | Yes | [56] |
MeQA | MeDIP-seq | Yes | Yes | Yes | No | No | Yes | [57] |
MeDUSA* | MeDIP-seq | Yes | Yes | Yes | Yes | No | Yes | |
msgbsR* | MRE-seq | Yes | No | Yes | Yes | Yes | Yes |