pTrimmer: An efficient tool to trim primers of multiplex deep sequencing data
pTrimmer: An efficient tool to trim primers of multiplex deep sequencing data
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pTrimmer：修剪多重深度测序数据引物的有效工具
DOI：
10.1186/s12859-019-2854-x
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发表时间：
2019-05-10
影响因子：
3
通讯作者：
Li, Zhiguang
中科院分区：
文献类型：
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作者：
Zhang, Xiaolong;Shao, Yanyan;Li, Zhiguang
随着多扩增子测序（multiple amplicon-sequencing， MAS）在遗传变异检测中的广泛应用，需要一种高效的工具从短读段中去除引物序列，以确保下游分析的可靠性。虽然目前有一些工具可用，但在高通量目标基因组测序中，它们的效率和准确性需要提高。考虑到MAS用于处理患者样本的潜在临床实施，这个问题变得更加紧迫。我们在这里开发了pTrimmer，可以同时处理数千个引物，大大提高了精度和性能。结果trimmer结合了k-mers和Needleman-Wunsch两种算法，即使存在测序误差也能保证其准确性。与同类工具相比，pTrimmer的灵敏度提高了28.59%，准确度提高了11.87%。仿真结果表明，与敏感度为70.85%、准确率为58.73%的cutPrimers相比，pTrimmer具有99.96%的超高灵敏度和97.38%的准确率。而pTrimmer的性能明显更高。每条线程的速度比cutPrimers快370倍，甚至比cutadapt快17000倍。从1100万个reads （Illumina PE 150 bp）中裁剪2158对引物只需要37秒，内存消耗不超过100 MB。结论sptrimmer可对多重扩增子序列和靶序列的引物序列进行裁剪。与其他三种类似的工具相比，它具有高度的敏感性和特异性，可以帮助用户获得更可靠的突变信息，用于下游分析。
BackgroundWith the widespread use of multiple amplicon-sequencing (MAS) in genetic variation detection, an efficient tool is required to remove primer sequences from short reads to ensure the reliability of downstream analysis. Although some tools are currently available, their efficiency and accuracy require improvement in trimming large scale of primers in high throughput target genome sequencing. This issue is becoming more urgent considering the potential clinical implementation of MAS for processing patient samples. We here developed pTrimmer that could handle thousands of primers simultaneously with greatly improved accuracy and performance.ResultpTrimmer combines the two algorithms of k-mers and Needleman-Wunsch algorithm, which ensures its accuracy even with the presence of sequencing errors. pTrimmer has an improvement of 28.59% sensitivity and 11.87% accuracy compared to the similar tools. The simulation showed pTrimmer has an ultra-high sensitivity rate of 99.96% and accuracy of 97.38% compared to cutPrimers (70.85% sensitivity rate and 58.73% accuracy). And the performance of pTrimmer is notably higher. It is about 370 times faster than cutPrimers and even 17,000 times faster than cutadapt per threads. Trimming 2158 pairs of primers from 11 million reads (Illumina PE 150 bp) takes only 37 s and no more than 100 MB of memory consumption.ConclusionspTrimmer is designed to trim primer sequence from multiplex amplicon sequencing and target sequencing. It is highly sensitive and specific compared to other three similar tools, which could help users to get more reliable mutational information for downstream analysis.