QPLOT: A Quality Assessment Tool for Next Generation Sequencing Data
QPLOT: A Quality Assessment Tool for Next Generation Sequencing Data
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DOI：
10.1155/2013/865181
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发表时间：
2013-01-01
影响因子：
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通讯作者：
Abecasis, Goncalo R.
中科院分区：
文献类型：
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作者：
Li, Bingshan;Zhan, Xiaowei;Abecasis, Goncalo R.
背景。下一代测序（NGS）被广泛用于鉴定与人类疾病相关的遗传变异。尽管这种方法具有成本效益，但底层数据容易受到许多类型错误的影响。重要的是，由于NGS技术和方案正在迅速发展，从样品制备到数据处理软件更新的步骤不断变化，因此使研究人员能够在下游分析之前常规评估测序和比对数据的质量非常重要。结果。在这里，我们描述QPLOT，一个自动化的工具，可以促进测序运行性能的质量评估。QPLOT将标准序列比对作为输入，生成一系列诊断指标，总结运行质量，并为这些指标生成方便的图形摘要。QPLOT计算效率高，可以生成网页，用于交互式探索详细结果，并且可以处理多个测序运行的联合输出。结论。QPLOT是一个自动化的工具，便于序列运行质量的评估。我们经常使用QPLOT来确保快速检测和诊断测序运行问题。我们希望QPLOT也能对社区有用。
Background. Next generation sequencing (NGS) is being widely used to identify genetic variants associated with human disease. Although the approach is cost effective, the underlying data is susceptible to many types of error. Importantly, since NGS technologies and protocols are rapidly evolving, with constantly changing steps ranging from sample preparation to data processing software updates, it is important to enable researchers to routinely assess the quality of sequencing and alignment data prior to downstream analyses. Results. Here we describe QPLOT, an automated tool that can facilitate the quality assessment of sequencing run performance. Taking standard sequence alignments as input, QPLOT generates a series of diagnostic metrics summarizing run quality and produces convenient graphical summaries for these metrics. QPLOT is computationally efficient, generates webpages for interactive exploration of detailed results, and can handle the joint output of many sequencing runs. Conclusion. QPLOT is an automated tool that facilitates assessment of sequence run quality. We routinely apply QPLOT to ensure quick detection of diagnostic of sequencing run problems. We hope that QPLOT will be useful to the community as well.