PEAT: an intelligent and efficient paired-end sequencing adapter trimming algorithm.
PEAT: an intelligent and efficient paired-end sequencing adapter trimming algorithm.
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DOI：
10.1186/1471-2105-16-s1-s2
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发表时间：
2015
影响因子：
3
通讯作者：
Hung JH
中科院分区：
文献类型：
--
作者：
Li YL;Weng JC;Hsiao CC;Chou MT;Tseng CW;Hung JH
在现代配对端测序方案中，短DNA片段导致适配器附加读取。目前的对端适配器去除方法是通过扫描读取端3'端的适配器片段来接近修剪适配器，这在某些应用中是不适用的。在这里，我们提出了一个快速和高度精确的适配器修剪算法，PEAT，专为对端测序设计。PEAT不需要先验的适配序列，便于大规模的元分析。我们在模拟和现实生活中的配对端测序文库中使用许多适配器修剪器评估了PEAT的性能。下游分析对RNA-seq、ChIP-seq和MNase-seq的影响说明了适配器修剪的重要性。几个有用的指导方针，应用适配器修剪与对准提出了建议。PEAT可以很容易地包含在常规的对端测序流水线中。PEAT的可执行二进制文件和独立的c++源代码包可以在网上免费获得。
In modern paired-end sequencing protocols short DNA fragments lead to adapter-appended reads. Current paired-end adapter removal approaches trim adapter by scanning the fragment of adapter on the 3' end of the reads, which are not competent in some applications. Here, we propose a fast and highly accurate adapter-trimming algorithm, PEAT, designed specifically for paired-end sequencing. PEAT requires no a priori adaptor sequence, which is convenient for large-scale meta-analyses. We assessed the performance of PEAT with many adapter trimmers in both simulated and real life paired-end sequencing libraries. The importance of adapter trimming was exemplified by the influence of the downstream analyses on RNA-seq, ChIP-seq and MNase-seq. Several useful guidelines of applying adapter trimmers with aligners were suggested. PEAT can be easily included in the routine paired-end sequencing pipeline. The executable binaries and the standalone C++ source code package of PEAT are freely available online.