Systematic and benchmarking studies of pipelines for mammal WGBS data in the novel NGS platform

Abstract

Abstract Background: Whole genome bisulfite sequencing(WGBS), possesses theaptitude to dissect methylation status at the nucleotide-level resolution of 5-methylcytosine(5mC) on a genome-wide scale. It is a powerful technique for epigenome in various cell types, and tissues. As a recently established next-generation sequencing(NGS) platform, GenoLab M is a promising alternative platform. However, its comprehensive evaluation for WGBS has not been reported. We sequenced two bisulfite-converted mammal DNA in this researchusing our GenoLab M and NovaSeq 6000, respectively. Then, we systematically compared those data via four widely used WGBS tools: BSMAP, Bismark, BatMeth2, and BS-Seeker2. We interrogated their computational time, genomedepth and coverage, and evaluated their percentage of methylated Cs. Result: Here, benchmarking a combination of pre- and post-processing methods, we found that trimming improved the performance of mapping efficiency in eight datasets. The data from two platformsuncovered ~80% of CpG sites genome-wide in the human cell line. Those data sequenced by GenoLab M achieved a far lower proportion of duplicates(~5.5%). Among pipelines, BSMAP provided an intriguing representation of 5mC distribution at CpG sites with 5mC levels >~78% in datasets from human cell lines, especially in the GenoLab M. BSMAP performed more advantages in running time, uniquely mapped reads percentages, genomic coverage, and quantitative accuracy. Finally, comparedwith 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 withthat from NovaSeq 6000. Conclusion: Together we confirmed that GenoLab M was a qualified NGS platform for WGBS with high performance. Our results showed that BSMAP was the suitable pipeline that allowed for WGBS studies on the GenoLab M platform.