Benchmarking DNA methylation analysis of 14 alignment algorithms for whole genome bisulfite sequencing in mammals.
Benchmarking DNA methylation analysis of 14 alignment algorithms for whole genome bisulfite sequencing in mammals.
复制标题
用于哺乳动物全基因组亚硫酸氢盐测序的 14 种比对算法的 DNA 甲基化基准分析
DOI：
10.1016/j.csbj.2022.08.051
复制
发表时间：
2022
影响因子：
6
通讯作者：
Yuan, Xiaolong
中科院分区：
文献类型：
--
作者：
Gong, Wentao;Pan, Xiangchun;Xu, Dantong;Ji, Guanyu;Wang, Yifei;Tian, Yuhan;Cai, Jiali;Li, Jiaqi;Zhang, Zhe;Yuan, Xiaolong
全基因组亚硫酸氢盐测序（WGBS）是甲基化组研究的重要技术。虽然已经开发了一系列工具来克服亚硫酸氢盐处理引起的映射挑战，但尚未对最新可用的工具在读取映射的性能以及在多种哺乳动物中的生物学见解进行评估。在此，基于147.7亿个读段的真实的和模拟的WGBS数据，我们进行了936个映射以基准和评估14个广泛使用的比对算法，从人、牛和猪的读段映射到生物学解释：Bwa-meth、BSBolt、BSMAP、Walt、Abismal、Batmeth 2、Hisat_3n、Hisat_3n_repeat、Bismark-bwt2-e2e、Bismark-his2、BSSeeker2-bwt、BSSeeker2-soap 2，BSSeeker 2-bwt 2-e2 e和BSSeeker 2-bwt 2-local。其中，Bwa-meth、BSBolt、BSMAP、Bismark-bwt 2-e2 e和Walt比对算法具有更高的独特定位读数、定位精度、召回率和F1评分，不同比对算法对甲基化组的影响在CpG位点的数量和甲基化水平、差异甲基化CpG（DMC）和区域（DMR）的调用上存在显著差异。此外，我们报道BSMAP在检测CpG坐标和甲基化水平，调用DMC，DMR，DMR相关基因和信号通路方面显示出最高的准确性。这些结果表明，仔细选择算法来描绘全基因组DNA甲基化是必要的，我们的工作为研究人员提供了有用的信息，选择比对算法，以有效地提高哺乳动物DNA甲基化检测的准确性。
Whole genome bisulfite sequencing (WGBS) is an essential technique for methylome studies. Although a series of tools have been developed to overcome the mapping challenges caused by bisulfite treatment, the latest available tools have not been evaluated on the performance of reads mapping as well as on biological insights in multiple mammals. Herein, based on the real and simulated WGBS data of 14.77 billion reads, we undertook 936 mappings to benchmark and evaluate 14 wildly utilized alignment algorithms from reads mapping to biological interpretation in humans, cattle and pigs: Bwa-meth, BSBolt, BSMAP, Walt, Abismal, Batmeth2, Hisat_3n, Hisat_3n_repeat, Bismark-bwt2-e2e, Bismark-his2, BSSeeker2-bwt, BSSeeker2-soap2, BSSeeker2-bwt2-e2e and BSSeeker2-bwt2-local. Specifically, Bwa-meth, BSBolt, BSMAP, Bismark-bwt2-e2e and Walt exhibited higher uniquely mapped reads, mapped precision, recall and F1 score than other nine alignment algorithms, and the influences of distinct alignment algorithms on the methylomes varied considerably at the numbers and methylation levels of CpG sites, the calling of differentially methylated CpGs (DMCs) and regions (DMRs). Moreover, we reported that BSMAP showed the highest accuracy at the detection of CpG coordinates and methylation levels, the calling of DMCs, DMRs, DMR-related genes and signaling pathways. These results suggested that careful selection of algorithms to profile the genome-wide DNA methylation is required, and our works provided investigators with useful information on the choice of alignment algorithms to effectively improve the DNA methylation detection accuracy in mammals.
登录
查看更多内容
影响因子：
4.8
作者：
Chatterton Z;Mendelev N;Chen S;Carr W;Kamimori GH;Ge Y;Dwork AJ;Haghighi F
通讯作者：
Haghighi F
影响因子：
14.9
作者：
Feng H;Conneely KN;Wu H
通讯作者：
Wu H
影响因子：
48
作者：
Langmead, Ben;Salzberg, Steven L.
通讯作者：
Salzberg, Steven L.
影响因子：
78.8
作者：
Koch, Alexander;Joosten, Sophie C.;van Engeland, Manon
通讯作者：
van Engeland, Manon
DOI：
10.1038/nrg2719
发表时间：
2010-03
期刊：
Nature reviews. Genetics
影响因子：
--
作者：
通讯作者：
--