We sequenced two bisulfite-converted mammal DNA in this research using our GenoLab M and NovaSeq 6000, respectively. Then, we systematically compared those data via four widely used WGBS tools (BSMAP, Bismark, BatMeth2, BS-Seeker2) and a new bisulfite-seq tool (BSBolt). We interrogated their computational time, genome depth and coverage, and evaluated their percentage of methylated Cs.
We found that those data sequenced by GenoLab M achieved a far lower proportion of duplicates (~ 5.5%), meaning that much more viable reads were obtained and used for the subsequent analysis procedures. Furthermore, compared with the previous methylation pattern of human cell line and mouse tissue, we confirmed that the data from GenoLab M performed similar consistency and accuracy in methylation levels of CpG sites with that from NovaSeq 6000. Hence, the research confirmed that BSMAP was the suitable pipeline that allowed for WGBS studies on the GenoLab M platform.