Fang, ChaoZhong, HuanziLin, YuxiangChen, BingHan, MoRen, HuahuiLu, HaorongLuber, JacobXia, MinLi, WangshengStein, ShaynaXu, XunZhang, WenweiDrmanac, RadojeWang, JianYang, HuanmingHammarström, LennartKostic, AleksandarKristiansen, KarstenLi, Junhua2018-04-192018Fang, C., H. Zhong, Y. Lin, B. Chen, M. Han, H. Ren, H. Lu, et al. 2018. “Assessment of the cPAS-based BGISEQ-500 platform for metagenomic sequencing.” GigaScience 7 (3): 1-8. doi:10.1093/gigascience/gix133. http://dx.doi.org/10.1093/gigascience/gix133.http://nrs.harvard.edu/urn-3:HUL.InstRepos:35982232Abstract Background: More extensive use of metagenomic shotgun sequencing in microbiome research relies on the development of high-throughput, cost-effective sequencing. Here we present a comprehensive evaluation of the performance of the new high-throughput sequencing platform BGISEQ-500 for metagenomic shotgun sequencing and compare its performance with that of 2 Illumina platforms. Findings: Using fecal samples from 20 healthy individuals, we evaluated the intra-platform reproducibility for metagenomic sequencing on the BGISEQ-500 platform in a setup comprising 8 library replicates and 8 sequencing replicates. Cross-platform consistency was evaluated by comparing 20 pairwise replicates on the BGISEQ-500 platform vs the Illumina HiSeq 2000 platform and the Illumina HiSeq 4000 platform. In addition, we compared the performance of the 2 Illumina platforms against each other. By a newly developed overall accuracy quality control method, an average of 82.45 million high-quality reads (96.06% of raw reads) per sample, with 90.56% of bases scoring Q30 and above, was obtained using the BGISEQ-500 platform. Quantitative analyses revealed extremely high reproducibility between BGISEQ-500 intra-platform replicates. Cross-platform replicates differed slightly more than intra-platform replicates, yet a high consistency was observed. Only a low percentage (2.02%–3.25%) of genes exhibited significant differences in relative abundance comparing the BGISEQ-500 and HiSeq platforms, with a bias toward genes with higher GC content being enriched on the HiSeq platforms. Conclusions: Our study provides the first set of performance metrics for human gut metagenomic sequencing data using BGISEQ-500. The high accuracy and technical reproducibility confirm the applicability of the new platform for metagenomic studies, though caution is still warranted when combining metagenomic data from different platforms.en-USBGISEQ-500quantitative metagenomic analysesnext-generation sequencingJournal Article2018-04-1910.1093/gigascience/gix133