In silico DNA sequence generation is a powerful technology to evaluate and validate bioinformatics tools, and accordingly more than 35 DNA sequence simulation tools have been developed. With such a diverse array of tools to choose from, an important question is: Which tool should be used for a desired outcome? This question is largely unanswered as documentation for many of these DNA simulation tools is sparse. To address this, we performed a review of DNA sequence simulation tools developed to date and evaluated 20 state-of-art DNA sequence simulation tools on their ability to produce accurate reads based on their implemented sequence error model. We provide a succinct description of each tool and suggest which tool is most appropriate for the given different scenarios. Given the multitude of similar yet non-identical tools, researchers can use this review as a guide to inform their choice of DNA sequence simulation tool. This paves the way towards assessing existing tools in a unified framework, as well as enabling different simulation scenario analysis within the same framework.

中文翻译：

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DNA序列数据模拟工具的广泛调查

在计算机中，DNA序列生成是一种强大的技术，可以评估和验证生物信息学工具，因此，已经开发了35种以上的DNA序列仿真工具。有这么多种工具可供选择，一个重要的问题是：应该使用哪种工具来获得理想的结果？由于许多此类DNA模拟工具的文档稀疏，因此该问题在很大程度上未得到解答。为了解决这个问题，我们对迄今为止开发的DNA序列仿真工具进行了综述，并评估了20种最新的DNA序列仿真工具基于其已实现的序列误差模型产生准确读数的能力。我们对每种工具进行了简要描述，并建议哪种工具最适合给定的不同场景。鉴于有许多类似但不相同的工具，研究人员可以以此综述为指导，告知他们选择DNA序列模拟工具的方法。这为评估统一框架中的现有工具铺平了道路，并在同一框架内实现了不同的仿真方案分析。