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

Area of Science:

• Microbiology
• Genomics
• Bioinformatics

Background:

• Metagenomic shotgun sequencing is crucial for microbiome research.
• High-throughput and cost-effective sequencing platforms are needed.
• The BGISEQ-500 is a new high-throughput sequencing platform.

Purpose of the Study:

• Evaluate the performance of the BGISEQ-500 platform for metagenomic shotgun sequencing.
• Compare BGISEQ-500 performance with Illumina HiSeq 2000 and HiSeq 4000 platforms.
• Assess intra-platform reproducibility and cross-platform consistency.

Main Methods:

• Used fecal samples from 20 healthy individuals.
• Performed intra-platform reproducibility tests with library and sequencing replicates on BGISEQ-500.
• Conducted cross-platform comparisons between BGISEQ-500 and two Illumina platforms.
• Utilized a novel overall accuracy quality control method.

Main Results:

• Obtained an average of 82.45 million high-quality reads per sample on BGISEQ-500 (96.06% of raw reads).
• Achieved 90.56% of bases scoring Q30 and above on BGISEQ-500.
• Demonstrated extremely high intra-platform reproducibility for BGISEQ-500.
• Observed high consistency across platforms, with only 2.02%-3.25% of genes showing significant abundance differences.
• Noted enrichment of higher GC content genes on Illumina HiSeq platforms.

Conclusions:

• The BGISEQ-500 platform offers high accuracy and technical reproducibility for human gut metagenomic sequencing.
• The platform is applicable for metagenomic studies.
• Caution is advised when combining metagenomic data generated from different sequencing platforms.