The CRISPR-Cas system has become a cutting-edge technology that revolutionized genome engineering. The use of Cas9 nuclease is currently the method of choice in most tasks requiring a specific DNA modification. The rapid development in the field of CRISPR-Cas is reflected by the constantly expanding ecosystem of computational tools aimed at facilitating experimental design and result analysis. The first group of CRISPR-Cas-related tools that we review is dedicated to aid in guide RNA design by prediction of their efficiency and specificity. The second, relatively new group of tools exploits the observed biases in repair outcomes to predict the results of CRISPR-Cas edits. The third class of tools is developed to assist in the evaluation of the editing outcomes by analysis of the sequencing data. These utilities are accompanied by relevant repositories and databases. Here we present a comprehensive and updated overview of the currently available CRISPR-Cas-related tools, from the perspective of a user who needs a convenient and reliable means to facilitate genome editing experiments at every step, from the guide RNA design to analysis of editing outcomes. Moreover, we discuss the current limitations and challenges that the field must overcome for further improvement in the CRISPR-Cas endeavor.

中文翻译：

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支持 CRISPR-Cas 实验的计算工具和资源。


CRISPR-Cas系统已成为彻底改变基因组工程的尖端技术。目前，大多数需要特定 DNA 修饰的任务都选择使用 Cas9 核酸酶。 CRISPR-Cas领域的快速发展体现在不断扩大的计算工具生态系统，旨在促进实验设计和结果分析。我们审查的第一组 CRISPR-Cas 相关工具致力于通过预测其效率和特异性来帮助指导 RNA 设计。第二组相对较新的工具利用修复结果中观察到的偏差来预测 CRISPR-Cas 编辑的结果。第三类工具的开发是为了通过分析测序数据来协助评估编辑结果。这些实用程序附带相关的存储库和数据库。在这里，我们从用户的角度对当前可用的 CRISPR-Cas 相关工具进行了全面和更新的概述，从指导 RNA 设计到编辑分析的每一步都需要方便可靠的手段来促进基因组编辑实验结果。此外，我们还讨论了该领域当前必须克服的限制和挑战，以进一步改进 CRISPR-Cas 的努力。