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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] (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