comparison of sequence reads obtained from three next-generation sequencing platforms比较序列读取来自三个下一代测序平台.pdf

Comparison of Sequence Reads Obtained from Three Next-Generation Sequencing Platforms 1. 1. 1 1 1,2,3 Shingo Suzuki , Naoaki Ono , Chikara Furusawa , Bei-Wen Ying , Tetsuya Yomo * 1 Department of Bioinformatics Engineering, Graduate School of Information Science and Technology, Suita, Osaka, Japan, 2 Exploratory Research for Advanced Technology (ERATO), Japan Science and Technology Agency, Suita, Osaka, Japan, 3 Graduate School of Frontier Biosciences, Osaka University, Suita, Osaka, Japan Abstract Next-generation sequencing technologies enable the rapid cost-effective production of sequence data. To evaluate the performance of these sequencing technologies, investigation of the quality of sequence reads obtained from these methods is important. In this study, we analyzed the quality of sequence reads and SNP detection performance using three commercially available next-generation sequencers, i.e., Roche Genome Sequencer FLX System (FLX), Illumina Genome Analyzer (GA), and Applied Biosystems SOLiD system (SOLiD). A common genomic DNA sample obtained from Escherichia coli strain DH1 was applied to these sequencers. The obtained sequence reads were aligned to the complete genome sequence of E. coli DH1, to evaluate the accuracy and sequence bias of these sequence methods. We found that the fraction of ‘‘junk’’ data, which could not be aligned to the reference genome, was largest in the data set of SOLiD, in which about half of reads could not be aligned. Among data sets after alignment to the reference, sequence accuracy was poorest in GA data sets, suggesting relatively low fidelity of the elongation reaction