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

BGISEQ-500 is a recently launched cPAS-based desktop sequencer, which has been used for RNA-seq and whole-genome sequencing. However, the performance of this high-throughput sequencing platform for metagenomic shotgun sequencing has not yet been evaluated.In this study, we generated a BGISEQ-500 metagenomic dataset from 20 healthy individuals including 8 sequencing replicates and 8 library replicates. By an in-house-developed overall-accuracy quality control method, BGISEQ-500 produced 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. Quantitative analyses revealed extremely high reproducibility between BGISEQ-500 intra-platform replicates. Furthermore, we assessed the inter-platform variation using 20 pairwise cross-platform replicates on BGISEQ-500 and Illumina HiSeq 2000 and demonstrated a high consistency between platforms. Only 11,354 (3.25%) genes showed reproducible significant differences in relative abundance between platforms, with a bias towards genes with higher GC content being enriched on the HiSeq 2000 platform.Our results demonstrate excellent intra-platform stability and inter-platform consistency for metagenomic data using the BGISEQ-500 platform validating the applicability of this new sequencing platform for quantitative metagenomic studies. We hope that you find our data and manuscript of general interest and sufficient quality to be considered for publication in GigaScience.