数字农科院2.0

Evaluation of Different SNP Analysis Software and Optimal Mining Process in Tree Species

文献类型： 外文期刊

作者： Mengjia Bu;Mengxuan Xu;Shentong Tao;Peng Cui;Bing He

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关键词： algorithm comparison;SNP calling protocol;SNP validation

期刊名称： Life

ISSN： 2075-1729

年卷期： 2023 年 13 卷 5 期

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收录情况： SCIE（2023版）

摘要： Single nucleotide polymorphism (SNP) is one of the most widely used molecular markers to help researchers understand the relationship between phenotypes and genotypes. SNP calling mainly consists of two steps, including read alignment and locus identification based on statistical models, and various software have been developed and applied in this issue. Meanwhile, in our study, very low agreement (<25%) was found among the prediction results generated by different software, which was much less consistent than expected. In order to obtain the optimal protocol of SNP mining in tree species, the algorithm principles of different alignment and SNP mining software were discussed in detail. And the prediction results were further validated based on in silico and experimental methods. In addition, hundreds of validated SNPs were provided along with some practical suggestions on program selection and accuracy improvement were provided, and we wish that these results could lay the foundation for the subsequent analysis of SNP mining.

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