SeqPurge: highly-sensitive adapter trimming for paired-end NGS data.
SeqPurge: highly-sensitive adapter trimming for paired-end NGS data.
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DOI：
10.1186/s12859-016-1069-7
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发表时间：
2016-05-10
影响因子：
3
通讯作者：
Bauer P
中科院分区：
文献类型：
--
作者：
Sturm M;Schroeder C;Bauer P
在NGS数据分析过程中，从短读取数据中修剪接头序列是一个常见的预处理步骤。当执行配对末端测序时，正向和反向读取之间的重叠可用于识别多余的适配序列。之前发布的几个适配器修剪工具利用了这一点。然而，我们对基于扩增的数据的评估表明，目前的大多数工具都不能删除所有的适配器序列，而且适配器污染甚至可能导致虚假的变体调用。在这里，我们介绍了https://github.com/imgag/ngs-bits)，(序列清除)，这是一种高度敏感的适配修剪器，它使用概率方法来检测Illumina测序数据的正向和反向读取之间的重叠。即使只有一个碱基长，SeqPurge也可以检测到非常短的适配器序列。与其他专门为配对端数据设计的适配器修剪器相比，我们发现SeqPurge实现了更高的敏感度。修剪后剩余的适配器底座数量最多可减少90%，具体取决于所比较的工具。在不同错误率下的仿真实验中，我们发现SeqPurge也是比较容错能力最强的适配器修剪器。SeqPurge实现了非常高的灵敏度和高容错性，并结合了可与其他最先进的适配器修剪器相媲美的特异性和运行时间。非常好的适配器修剪性能，再加上基于质量的修剪和基本质量控制等附加功能，使SeqPurge成为对端NGS数据进行预处理的极佳选择。本文的在线版本(doi：10.1186/s12859-0161069-7)包含补充材料，授权用户可以使用。
Trimming of adapter sequences from short read data is a common preprocessing step during NGS data analysis. When performing paired-end sequencing, the overlap between forward and reverse read can be used to identify excess adapter sequences. This is exploited by several previously published adapter trimming tools. However, our evaluation on amplicon-based data shows that most of the current tools are not able to remove all adapter sequences and that adapter contamination may even lead to spurious variant calls. Here we present SeqPurge (https://github.com/imgag/ngs-bits), a highly-sensitive adapter trimmer that uses a probabilistic approach to detect the overlap between forward and reverse reads of Illumina sequencing data. SeqPurge can detect very short adapter sequences, even if only one base long. Compared to other adapter trimmers specifically designed for paired-end data, we found that SeqPurge achieves a higher sensitivity. The number of remaining adapter bases after trimming is reduced by up to 90 %, depending on the compared tool. In simulations with different error rates, we found that SeqPurge is also the most error-tolerant adapter trimmer in the comparison. SeqPurge achieves a very high sensitivity and a high error-tolerance, combined with a specificity and runtime that are comparable to other state-of-the-art adapter trimmers. The very good adapter trimming performance, complemented with additional features such as quality-based trimming and basic quality control, makes SeqPurge an excellent choice for the pre-processing of paired-end NGS data. The online version of this article (doi:10.1186/s12859-016-1069-7) contains supplementary material, which is available to authorized users.