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Table 1 Selected tools and their features. Whether the pipeline is capable of performing an analysis from raw reads to DMRs and DMPs was a crucial criterion for the selection of tools. However, other aspects, such as graphic output and availability of a detailed manual, were also important for the final recommendation

From: DNA methylation data by sequencing: experimental approaches and recommendations for tools and pipelines for data analysis

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

[43, 58]

msgbsR*

MRE-seq

Yes

No

Yes

Yes

Yes

Yes

[44, 59]

  1. *Recommended
  2. Tab-del, tab-delimited output