用于多重PCR甲基化靶向测序的比对软件性能评估  

Performance Evaluation of Mapping Tools for Methylated Multiple PCR Targeted Sequencing

作　　者：林俊杰 郑琳琳 周宇荀[1] 李凯[1] 肖君华[1] LIN Junjie;ZHENG Linlin;ZHOU Yuxun;LI Kai;XIAO Junhua(College of Biological Science and Medical Engineering,Donghua University,Shanghai,201620)

机构地区：[1]东华大学生物与医学工程学院,上海201620

出　　处：《基因组学与应用生物学》2024年第4期719-728,共10页Genomics and Applied Biology

基　　金：国家重点研发计划(2018YFA0801101)资助。

摘　　要：多重PCR甲基化靶向测序数据尚缺乏针对性的比对软件。本研究评估了9种比对方案在处理多重PCR甲基化靶向测序数据时的性能,包括平均CPU运行时间、平均最大内存、平均比对率、F1分数、平均比对速率、比对未通过率和差异甲基化位点,以及比对率受亚硫酸氢盐转化率和测序错误率的影响。本研究建立了打分系统以综合评价比对方案的优劣,结果显示,排名前三的方案依次为Bismarkbwt2(8.098分)、BWA-meth(7.846分)和Bismarkbwt1(7.840分)。这三个方案的F1分数均为1.000,且在不同亚硫酸氢盐转化率和测序错误率下的比对率表现最优。此外,Bismarkbwt2还对应最多的差异甲基化位点和最低的比对未通过率,并在平均最大内存和平均比对率两项指标上表现良好。因此,本研究推荐Bowtie2模式下的Bismark作为后续搭建多重PCR甲基化靶向测序生物信息学分析流程的比对软件。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,F1-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 Bismarkbwt2(8.098 points),BWA-meth(7.846 points),and Bismarkbwt1(7.840 points).All three schemes had a F1-score of 1.000,and they performed optimally in terms of mapping rate at different bisulfite conversion rates and sequencing error rates.In addition,Bismarkbwt2 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.

关 键 词：DNA甲基化 多重PCR甲基化靶向测序 比对方案 序列比对 软件性能 

分 类 号：Q811.4[生物学—生物工程]