title: A reference human genome dataset of the BGISEQ-500 sequencer.
abstract: BGISEQ-500 is a new desktop sequencer developed by BGI. Using DNA nanoball and combinational probe anchor synthesis developed from Complete Genomics™ sequencing technologies, it generates short reads at a large scale. Here, we present the first human whole-genome sequencing dataset of BGISEQ-500. The dataset was generated by sequencing the widely used cell line HG001 (NA12878) in two sequencing runs of paired-end 50 bp (PE50) and two sequencing runs of paired-end 100 bp (PE100). We also include examples of the raw images from the sequencer for reference. Finally, we identified variations using this dataset, estimated the accuracy of the variations, and compared to that of the variations identified from similar amounts of publicly available HiSeq2500 data. We found similar single nucleotide polymorphism (SNP) detection accuracy for the BGISEQ-500 PE100 data (false positive rate [FPR] = 0.00020%, sensitivity = 96.20%) compared to the PE150 HiSeq2500 data (FPR = 0.00017%, sensitivity = 96.60%) better SNP detection accuracy than the PE50 data (FPR = 0.0006%, sensitivity = 94.15%). But for insertions and deletions (indels), we found lower accuracy for BGISEQ-500 data (FPR = 0.00069% and 0.00067% for PE100 and PE50 respectively, sensitivity = 88.52% and 70.93%) than the HiSeq2500 data (FPR = 0.00032%, sensitivity = 96.28%). Our dataset can serve as the reference dataset, providing basic information not just for future development, but also for all research and applications based on the new sequencing platform.
authors.affiliation: National Institutes for food and drug Control (NIFDC), No.2, Tiantan Xili Dongcheng District, Beijing 10050, P. R. China.
authors.forename: Jie
authors.initials: J
authors.lastname: Huang
authors.affiliation: BGI-Shenzhen, Bei Shan Industrial Zone, Yantian District, Shenzhen, Guangdong Province, 518083, P. R. China.
authors.forename: Xinming
authors.initials: X
authors.lastname: Liang
authors.affiliation: State Food and Drug Administration Hubei Center for Medical Equipment Quality Supervision and Testing, 24-9, Zhongbei East Road, Wuhan, Hubei Province, 430000, P. R. China.
authors.forename: Yuankai
authors.initials: Y
authors.lastname: Xuan
authors.affiliation: BGI-Shenzhen, Bei Shan Industrial Zone, Yantian District, Shenzhen, Guangdong Province, 518083, P. R. China.
authors.forename: Chunyu
authors.initials: C
authors.lastname: Geng
authors.affiliation: BGI-Shenzhen, Bei Shan Industrial Zone, Yantian District, Shenzhen, Guangdong Province, 518083, P. R. China.
authors.forename: Yuxiang
authors.initials: Y
authors.lastname: Li
authors.affiliation: BGI-Shenzhen, Bei Shan Industrial Zone, Yantian District, Shenzhen, Guangdong Province, 518083, P. R. China.
authors.forename: Haorong
authors.initials: H
authors.lastname: Lu
authors.affiliation: National Institutes for food and drug Control (NIFDC), No.2, Tiantan Xili Dongcheng District, Beijing 10050, P. R. China.
authors.forename: Shoufang
authors.initials: S
authors.lastname: Qu
authors.affiliation: State Food and Drug Administration Hubei Center for Medical Equipment Quality Supervision and Testing, 24-9, Zhongbei East Road, Wuhan, Hubei Province, 430000, P. R. China.
authors.forename: Xianglin
authors.initials: X
authors.lastname: Mei
authors.affiliation: National Institutes for food and drug Control (NIFDC), No.2, Tiantan Xili Dongcheng District, Beijing 10050, P. R. China.
authors.forename: Hongbo
authors.initials: H
authors.lastname: Chen
authors.affiliation: National Institutes for food and drug Control (NIFDC), No.2, Tiantan Xili Dongcheng District, Beijing 10050, P. R. China.
authors.forename: Ting
authors.initials: T
authors.lastname: Yu
authors.affiliation: National Institutes for food and drug Control (NIFDC), No.2, Tiantan Xili Dongcheng District, Beijing 10050, P. R. China.
authors.forename: Nan
authors.initials: N
authors.lastname: Sun
authors.affiliation: BGI-Shenzhen, Bei Shan Industrial Zone, Yantian District, Shenzhen, Guangdong Province, 518083, P. R. China.
authors.forename: Junhua
authors.initials: J
authors.lastname: Rao
authors.affiliation: BGI-Qingdao, Tuanjie Rd., Huangdao District, Qingdao, Shandong Province, 266555, P. R. China.
authors.forename: Jiahao
authors.initials: J
authors.lastname: Wang
authors.affiliation: BGI-Shenzhen, Bei Shan Industrial Zone, Yantian District, Shenzhen, Guangdong Province, 518083, P. R. China.
authors.forename: Wenwei
authors.initials: W
authors.lastname: Zhang
authors.affiliation: BGI-Shenzhen, Bei Shan Industrial Zone, Yantian District, Shenzhen, Guangdong Province, 518083, P. R. China.
authors.forename: Ying
authors.initials: Y
authors.lastname: Chen
authors.affiliation: BGI-Shenzhen, Bei Shan Industrial Zone, Yantian District, Shenzhen, Guangdong Province, 518083, P. R. China.
authors.forename: Sha
authors.initials: S
authors.lastname: Liao
authors.affiliation: BGI-Shenzhen, Bei Shan Industrial Zone, Yantian District, Shenzhen, Guangdong Province, 518083, P. R. China.
authors.forename: Hui
authors.initials: H
authors.lastname: Jiang
authors.affiliation: BGI-Shenzhen, Bei Shan Industrial Zone, Yantian District, Shenzhen, Guangdong Province, 518083, P. R. China.
authors.forename: Xin
authors.initials: X
authors.lastname: Liu
authors.affiliation: National Institutes for food and drug Control (NIFDC), No.2, Tiantan Xili Dongcheng District, Beijing 10050, P. R. China.
authors.forename: Zhaopeng
authors.initials: Z
authors.lastname: Yang
authors.affiliation: BGI-Shenzhen, Bei Shan Industrial Zone, Yantian District, Shenzhen, Guangdong Province, 518083, P. R. China.
authors.forename: Feng
authors.initials: F
authors.lastname: Mu
authors.affiliation: National Institutes for food and drug Control (NIFDC), No.2, Tiantan Xili Dongcheng District, Beijing 10050, P. R. China.
authors.forename: Shangxian
authors.initials: S
authors.lastname: Gao
mesh_terms: D002460:Cell Line; D015723:Gene Library; D015894:Genome, Human; D006801:Humans; D020641:Polymorphism, Single Nucleotide; D017422:Sequence Analysis, DNA
keywords: BGISEQ-500; genomics; next-generation sequencing; sequencing