Sentieon DNASeq Variant Calling Workflow Demonstrates Strong Computational Performance and Accuracy
Sentieon DNASeq Variant Calling Workflow Demonstrates Strong Computational Performance and Accuracy
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DOI：
10.3389/fgene.2019.00736
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发表时间：
2019-08-20
影响因子：
3.7
通讯作者：
Mainzer, Liudmila S.
中科院分区：
文献类型：
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作者：
Kendig, Katherine, I;Baheti, Saurabh;Mainzer, Liudmila S.
随着可靠、高效的基因组测序变得无处不在，对同样可靠、高效的变异召唤的需求变得越来越重要。由Broad研究所维护的基因组分析工具包（GATK）是目前被广泛接受的变体调用软件标准。然而，替代解决方案可以在不牺牲准确性的情况下提供更快的变量调用。其中一个替代方案是Sentieon DNASeq，这是一个类似于GATK的工具包，但构建在高度优化的后端上。我们对DNASeq单样本变体调用管道进行了独立评估，并与GATK进行了比较。我们的结果支持两个软件包几乎相同的准确性，展示了Sentieon的最佳可扩展性和高速度，并描述了部署DNASeq的计算性能考虑因素。
As reliable, efficient genome sequencing becomes ubiquitous, the need for similarly reliable and efficient variant calling becomes increasingly important. The Genome Analysis Toolkit (GATK), maintained by the Broad Institute, is currently the widely accepted standard for variant calling software. However, alternative solutions may provide faster variant calling without sacrificing accuracy. One such alternative is Sentieon DNASeq, a toolkit analogous to GATK but built on a highly optimized backend. We conducted an independent evaluation of the DNASeq single-sample variant calling pipeline in comparison to that of GATK. Our results support the near-identical accuracy of the two software packages, showcase optimal scalability and great speed from Sentieon, and describe computational performance considerations for the deployment of DNASeq.