Sequencing error profiles of Illumina sequencing instruments.
Sequencing error profiles of Illumina sequencing instruments.
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Illumina测序仪器的测序错误概况。
DOI：
10.1093/nargab/lqab019
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发表时间：
2021-03
影响因子：
4.6
通讯作者：
Nekrutenko A
中科院分区：
文献类型：
--
作者：
Stoler N;Nekrutenko A
测序技术在过去十年中取得了巨大的进步。先前的研究表明，特定仪器在受控条件下的质量。在这里，我们开发了一种能够追溯确定大多数公共测序数据集错误率的方法。为了做到这一点，我们利用了读取之间的重叠，这是许多测序库的一个特征。用这种方法，我们调查了来自Illumina生产的7种不同测序仪器的1943个不同的数据集。我们发现，在公共数据集中，HiSeq和NovaSeq等更昂贵的平台具有更低的错误率和更少的变化。但我们也发现，在每个平台上都有很大的差异，测序实验的准确性很大程度上取决于实验者。我们展示了序列上下文的重要性，特别是前面的碱基偏向后面的碱基的现象。我们还展示了仪器之间序列偏差模式的差异。与基于基础化学的预期相反，HiSeq X 10和NovaSeq 6000在先验基础偏差方面有明显的例外。我们的结果表明了每个测序实验的具体情况的重要性，以及评估每个测序实验质量的重要性。
Sequencing technology has achieved great advances in the past decade. Studies have previously shown the quality of specific instruments in controlled conditions. Here, we developed a method able to retroactively determine the error rate of most public sequencing datasets. To do this, we utilized the overlaps between reads that are a feature of many sequencing libraries. With this method, we surveyed 1943 different datasets from seven different sequencing instruments produced by Illumina. We show that among public datasets, the more expensive platforms like HiSeq and NovaSeq have a lower error rate and less variation. But we also discovered that there is great variation within each platform, with the accuracy of a sequencing experiment depending greatly on the experimenter. We show the importance of sequence context, especially the phenomenon where preceding bases bias the following bases toward the same identity. We also show the difference in patterns of sequence bias between instruments. Contrary to expectations based on the underlying chemistry, HiSeq X Ten and NovaSeq 6000 share notable exceptions to the preceding-base bias. Our results demonstrate the importance of the specific circumstances of every sequencing experiment, and the importance of evaluating the quality of each one.