Assessment of the cPAS-based BGISEQ-500 platform for metagenomic sequencing

Citation:

Chao Fang, Huanzi Zhong, Yuxiang Lin, Bin Chen, Mo Han, Huahui Ren, Haorong Lu, Jacob Mayne Luber, Min Xia, Wangsheng Li, Shayna Stein, Xun Xu, Wenwei Zhang, Radoje Drmanac, Jian Wang, Huanming Yang, Lennart Hammarström, Aleksandar David Kostic, Karsten Kristiansen, and Junhua Li. 2017. “Assessment of the cPAS-based BGISEQ-500 platform for metagenomic sequencing.” Gigascience.

Abstract:

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 two 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 versus the Illumina HiSeq 2000 platform and the Illumina HiSeq 4000 platform. In addition, we compared the performance of the two 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 towards genes with higher GC content being enriched on the HiSeq platforms. Conclusion: 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.