cutPrimers: A New Tool for Accurate Cutting of Primers from Reads of Targeted Next Generation Sequencing
cutPrimers: A New Tool for Accurate Cutting of Primers from Reads of Targeted Next Generation Sequencing
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DOI：
10.1089/cmb.2017.0096
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发表时间：
2017-11-01
影响因子：
1.7
通讯作者：
Filipenko, Maxim
中科院分区：
文献类型：
--
作者：
Kechin, Andrey;Boyarskikh, Uljana;Filipenko, Maxim
从读段切割引物是处理基于靶向扩增子的下一代测序数据的重要步骤。现有的工具适于从读段切割一个或几个引物/衔接子序列并去除它们的所有出现。此外，大多数现有工具使用kmers，并且可能仅切割部分引物或具有所研究的基因序列的引物。因此，使用此类程序会导致不正确的修剪、覆盖率降低以及假阳性和/或假阴性结果的数量增加。我们开发了一种名为cutPrimers的新工具，用于从读取中准确切割任何数量的引物。使用在BRCA 1/2基因研究期间获得的测序读数，我们将其与cutadapt，AlienTrimmer和BBDuk进行了比较。所有这些都以这样的方式修剪读段，使得至少两个扩增子的覆盖度降低到不可接受的水平（
Cutting of primers from reads is an important step of processing targeted amplicon-based next generation sequencing data. Existing tools are adapted for cutting of one or several primer/adapter sequences from reads and removing all of their occurrences. Also most of the existing tools use kmers and may cut only part of primers or primers with studied sequence of gene. Because of this, use of such programs leads to incorrect trimming, reduction of coverage, and increase in the number of false-positive and/or false-negative results. We have developed a new tool named cutPrimers for accurate cutting of any number of primers from reads. Using sequencing reads that were obtained during study of BRCA1/2 genes, we compared it with cutadapt, AlienTrimmer, and BBDuk. All of them trimmed reads in such a way that coverage of at least two amplicons decreased to unacceptable level (