Evaluation of alignment algorithms for discovery and identification of pathogens using RNA-Seq.
Evaluation of alignment algorithms for discovery and identification of pathogens using RNA-Seq.
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DOI：
10.1371/journal.pone.0076935
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发表时间：
2013
期刊：
影响因子：
3.7
通讯作者：
Ferretti V
中科院分区：
文献类型：
--
作者：
Borozan I;Watt SN;Ferretti V
下一代测序技术为已知和新型病毒的表征和发现提供了无与伦比的机会。由于已知病毒与真核生物和细菌生物相比具有最高的突变率，因此我们评估了11种众所周知的比对算法（BLAST、BLAT、BWA、BWA-SW、BWA-MEM、BFAST、Bowtie 2、Novoalign、GSNAP、SHRiMP 2和星星）可用于表征转录组样本中突变和非突变病毒序列（包括表现出RNA剪接的序列）的程度。为了客观地评估比对器，我们开发了一个现实的RNA-Seq模拟和评估框架（RiSER），并提出了一个新的组合评分来对比对器进行排序，以根据其精确度，灵敏度和比对准确度进行病毒表征。我们使用RiSER模拟人类和病毒读取序列，并建议用于人类转录组样品中病毒序列表征的最佳比对器集。我们的研究结果表明，在比对器之间存在显著和实质性的差异，并且基于数字减影的病毒识别框架可以并且应该在过程的不同部分使用不同的比对器。我们确定了突变病毒序列可以有效表征的程度，并表明更敏感的比对，如BLAST，BFAST，SHRiMP 2，BWA-SW和GSNAP可以准确地表征基本上不同的病毒序列，总序列突变率高达15%。我们相信，这里提出的结果将是有用的研究人员选择比对病毒序列表征使用下一代测序数据。
Next-generation sequencing technologies provide an unparallelled opportunity for the characterization and discovery of known and novel viruses. Because viruses are known to have the highest mutation rates when compared to eukaryotic and bacterial organisms, we assess the extent to which eleven well-known alignment algorithms (BLAST, BLAT, BWA, BWA-SW, BWA-MEM, BFAST, Bowtie2, Novoalign, GSNAP, SHRiMP2 and STAR) can be used for characterizing mutated and non-mutated viral sequences - including those that exhibit RNA splicing - in transcriptome samples. To evaluate aligners objectively we developed a realistic RNA-Seq simulation and evaluation framework (RiSER) and propose a new combined score to rank aligners for viral characterization in terms of their precision, sensitivity and alignment accuracy. We used RiSER to simulate both human and viral read sequences and suggest the best set of aligners for viral sequence characterization in human transcriptome samples. Our results show that significant and substantial differences exist between aligners and that a digital-subtraction-based viral identification framework can and should use different aligners for different parts of the process. We determine the extent to which mutated viral sequences can be effectively characterized and show that more sensitive aligners such as BLAST, BFAST, SHRiMP2, BWA-SW and GSNAP can accurately characterize substantially divergent viral sequences with up to 15% overall sequence mutation rate. We believe that the results presented here will be useful to researchers choosing aligners for viral sequence characterization using next-generation sequencing data.
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影响因子：
3
作者：
Borozan I;Wilson S;Blanchette P;Laflamme P;Watt SN;Krzyzanowski PM;Sircoulomb F;Rottapel R;Branton PE;Ferretti V
通讯作者：
Ferretti V
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