quast 的结果怎么看_使用quast评估基因组装配的质量

quast 的结果怎么看

The assembly algorithms that have been developed so far intend to provide better assemblies evaluated under different criteria. Hence, depending on the specific scenario the assembly process might produce better results if we use the most appropriate assembler. Even though contiguous genomes may not be produced, segments from the reference genomes can be obtained using existing assembly methods. Therefore, the need to evaluate the quality of assemblies exists. These evaluations help researchers to pick different assemblers for different scenarios.

到目前为止已开发的组装算法旨在提供在不同标准下评估的更好的组装。 因此，根据具体情况，如果使用最合适的汇编程序，则汇编过程可能会产生更好的结果。 即使可能不会产生连续的基因组，也可以使用现有的组装方法从参考基因组中获得片段。 因此，存在评估装配质量的需求。 这些评估有助于研究人员针对不同的情况选择不同的组装商。

How can we know whether the assemblies we obtain from reads using currently available assemblers are correct or not? In this article, we will see how to determine the quality of assemblies using QUAST, which is one of the most famous assessment tools available for genome assemblies. Let’s get started.

我们如何知道我们使用当前可用的汇编程序读取的汇编程序是否正确？ 在本文中，我们将看到如何使用QUAST来确定装配的质量， QUAST是可用于基因组装配的最著名的评估工具之一。 让我们开始吧。

什么是QUAST？ (What is QUAST?)

QUAST stands for QUality Assessment Tool. QUAST can evaluate assemblies using reference genomes, as well as without reference genomes. QUAST produces detailed reports, tables and plots which show the different aspects of assemblies.

QUAST代表质量评估工具。 QUAST可以使用参考基因​​组以及不使用参考基因​​组来评估装配。 QUAST生成详细的报告，表格和图解，以显示装配的不同方面。

下载QUAST (Download QUAST)

You can go to the official website of QUAST and click on the DOWNLOAD button.

您可以访问QUAST的官方网站，然后单击“ 下载”按钮。

You will be directed to a SOURCEFORGE download page from where you can download the latest version (quast-5.0.2 when I was writing this article) of QUAST. The pre-compiled binaries will be downloaded and you can run it straight away after extracting.

您将被引导到SOURCEFORGE下载页面，从该页面可以下载QUAST的最新版本(我写本文时为quast-5.0.2 )。 预编译的二进制文件将被下载，提取后您可以立即运行它。

tar -xf quast-5.0.2.tar.gz
cd quast-5.0.2
quast.py

You can see the following after executing quast.py or python quast.py.

执行quast.py或python quast.py之后，您可以看到