Performance Evaluation of Mapping Tools for Methylated Multiple PCR Targe-ted Sequencing
There is currently a lack of mapping tools for methylated multiple PCR targeted sequencing data.This study evaluated the performance of nine mapping methods including average CPU running time,average maximum memory,average mapping rate,Fl-score,average mapping speed,mapping failure rate,differential methylation site,bisulfite conversion rate and sequencing error rate on its corresponding mapping rate when processing methylated multiple PCR targeted sequencing data.A scoring system was established to comprehensively evaluate the performance of these mapping methods,and the results showed that the top three methods were Bismarkb-wt2(8.098 points),BWA-meth(7.846 points),and Bismarkbwtl(7.840 points).All three schemes had a Fl-score of 1.000,and they performed optimally in terms of mapping rate at different bisulfite conversion rates and sequencing error rates.In addition,Bis-markbwt2 corresponded to the highest number of differential methylation sites and the lowest mapping failure rate,and performed well on the ave-rage maximum memory and average mapping rate.Therefore,this study recommends Bismark under the Bowtie2 mode as the mapping tools for the construction of bioinformatics analysis process to the methylated multiple PCR targeted sequencing.
DNA methylationMethylated multiple PCR targeted sequencingMapping methodsSequence alignmentTools perfor-mance
NETL
NSTL
万方数据
