Unknown

Dataset Information

0

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


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 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.

SUBMITTER: Fang C 

PROVIDER: S-EPMC5848809 | biostudies-literature | 2018 Mar

REPOSITORIES: biostudies-literature

altmetric image

Publications


<h4>Background</h4>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.<h4>Findings</h4>Using fecal samples from 20 healthy individuals, we evaluated the intra-platform reproducibility f  ...[more]

Similar Datasets

| S-EPMC7448675 | biostudies-literature
| S-EPMC6709004 | biostudies-literature
| S-EPMC5570000 | biostudies-literature
| S-EPMC5761881 | biostudies-literature
| S-EPMC6088413 | biostudies-literature
| S-EPMC5467036 | biostudies-literature
| PRJEB19427 | ENA
| PRJEB19426 | ENA
| S-EPMC6857306 | biostudies-literature
| PRJEB19428 | ENA