SHI7 Is a Self-Learning Pipeline for Multipurpose Short-Read DNA Quality Control
SHI7 Is a Self-Learning Pipeline for Multipurpose Short-Read DNA Quality Control
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DOI：
10.1128/msystems.00202-17
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发表时间：
2018-05-01
期刊：
影响因子：
6.4
通讯作者：
Knights, Dan
中科院分区：
文献类型：
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作者：
Al-Ghalith, Gabriel A.;Hillmann, Benjamin;Knights, Dan
下一代测序技术对于许多生物学科都非常重要;然而，由于技术和生物学的限制，现代测序仪产生的短DNA序列需要大量的质量控制（QC）措施来减少错误，去除技术污染物，或将双端读段合并在一起成为更长或更高质量的重叠群。每个步骤都有许多工具，但选择适当的方法和使用参数可能具有挑战性，因为每个步骤的参数化取决于所使用的测序技术的特殊性，分析的样品类型以及仪器和样品制备的随机性。此外，最终用户可能不知道关于其数据如何生成的所有相关信息，例如双端序列的预期重叠或用于做出明智选择的衔接子类型。这种日益增加的复杂性和细微差别需要一个管道，以用户友好的方式将现有步骤组合在一起，并在可能的情况下自动从数据中学习合理的质量参数。我们提出了一个用户友好的质量控制管道称为SHI 7（规范发音为“shizen”），其旨在通过预测常见测序衔接子的存在和/或类型、要修剪的质量分数、数据集是鸟枪测序还是扩增子测序、读段是配对末端还是单末端以及对是否可重复来简化终端用户的短读段数据的质量控制，包括对重叠的预期量。我们希望SHI 7能让所有的研究人员，无论是专家还是新手，都能更容易地遵循合理的实践来进行短读段数据的质量控制。重要信息高通量DNA测序数据的质量控制是一项重要但有时很费力的任务，需要使用测序方案的背景知识（如接头类型、测序技术、插入片段大小/可重复性、配对末端性等）。质量控制协议通常需要应用这些背景知识来选择和执行具有适当参数的许多质量控制步骤，这在使用公共数据或来自使用不同协议的合作者的数据时尤其困难。我们已经创建了一个精简的质量控制管道，旨在大大简化从原始机器输出文件到可操作序列数据的DNA质量控制过程。与其他方法相比，我们提出的管道易于安装和使用，并尝试通过单个命令自动从数据中学习必要的参数。
Next-generation sequencing technology is of great importance for many biological disciplines; however, due to technical and biological limitations, the short DNA sequences produced by modern sequencers require numerous quality control (QC) measures to reduce errors, remove technical contaminants, or merge paired-end reads together into longer or higher-quality contigs. Many tools for each step exist, but choosing the appropriate methods and usage parameters can be challenging because the parameterization of each step depends on the particularities of the sequencing technology used, the type of samples being analyzed, and the stochasticity of the instrumentation and sample preparation. Furthermore, end users may not know all of the relevant information about how their data were generated, such as the expected overlap for paired-end sequences or type of adaptors used to make informed choices. This increasing complexity and nuance demand a pipeline that combines existing steps together in a user-friendly way and, when possible, learns reasonable quality parameters from the data automatically. We propose a user-friendly quality control pipeline called SHI7 (canonically pronounced "shizen"), which aims to simplify quality control of short-read data for the end user by predicting presence and/or type of common sequencing adaptors, what quality scores to trim, whether the data set is shotgun or amplicon sequencing, whether reads are paired end or single end, and whether pairs are stitchable, including the expected amount of pair overlap. We hope that SHI7 will make it easier for all researchers, expert and novice alike, to follow reasonable practices for short-read data quality control.IMPORTANCE Quality control of high-throughput DNA sequencing data is an important but sometimes laborious task requiring background knowledge of the sequencing protocol used (such as adaptor type, sequencing technology, insert size/stitchability, paired-endedness, etc.). Quality control protocols typically require applying this background knowledge to selecting and executing numerous quality control steps with the appropriate parameters, which is especially difficult when working with public data or data from collaborators who use different protocols. We have created a streamlined quality control pipeline intended to substantially simplify the process of DNA quality control from raw machine output files to actionable sequence data. In contrast to other methods, our proposed pipeline is easy to install and use and attempts to learn the necessary parameters from the data automatically with a single command.